vela-protocol 0.112.0

use crate::{
    benchmark, bridge, bundle, carina_validate, conformance, decision, diff, events, export,
    frontier_repo, impact, lint, normalize, packet, project, propagate, proposals, repo, review,
    search, serve, sign, signals, sources, state, state_integrity, tensions, validate,
};

use std::collections::BTreeMap;
use std::future::Future;
use std::path::{Path, PathBuf};
use std::pin::Pin;
use std::sync::OnceLock;

use clap::{Parser, Subcommand};
use colored::Colorize;

use crate::cli_style as style;
use reqwest::Client;
use serde::Serialize;
use serde_json::{Value, json};
use sha2::{Digest, Sha256};

#[derive(Parser)]
#[command(name = "vela", version)]
#[command(about = "Portable frontier state for science")]
struct Cli {
    #[command(subcommand)]
    command: Commands,
}

#[derive(Subcommand)]
enum Commands {
    /// v0.22 Agent Inbox: run Literature Scout against a folder of
    /// PDFs. Each candidate finding becomes a `finding.add`
    /// `StateProposal` tagged with the scout's `AgentRun`, written
    /// to the frontier's `proposals` array. Reviewers accept or
    /// reject in the Workbench Inbox; nothing becomes a canonical
    /// finding without a signed accept.
    Scout {
        /// Folder of PDFs to read.
        folder: PathBuf,
        /// Frontier file the proposals are appended to.
        #[arg(long)]
        frontier: PathBuf,
        /// LLM backend override (matches `vela ingest --backend`).
        #[arg(short, long)]
        backend: Option<String>,
        /// Preview without writing to the frontier file.
        #[arg(long)]
        dry_run: bool,
        /// Output stable JSON for programmatic callers.
        #[arg(long)]
        json: bool,
    },
    /// v0.23 Agent Inbox: run Notes Compiler against a folder of
    /// Markdown / Obsidian notes. Each open question, hypothesis,
    /// candidate finding, or tension becomes a `finding.add`
    /// `StateProposal` tagged with the compiler's `AgentRun`,
    /// written to the frontier's `proposals` array. Same review
    /// loop as Literature Scout.
    CompileNotes {
        /// Vault or folder of Markdown notes to read.
        vault: PathBuf,
        /// Frontier file the proposals are appended to.
        #[arg(long)]
        frontier: PathBuf,
        /// Optional model alias (`sonnet`, `opus`, …).
        #[arg(short, long)]
        backend: Option<String>,
        /// Cap on files processed (default 50).
        #[arg(long)]
        max_files: Option<usize>,
        /// Per-note cap on items emitted in *each* category
        /// (open_questions / hypotheses / candidate_findings /
        /// tensions). Default 4. Trims the strongest items the model
        /// returns so dense notes don't drown the Inbox.
        #[arg(long)]
        max_items_per_category: Option<usize>,
        /// Preview without writing to the frontier file.
        #[arg(long)]
        dry_run: bool,
        /// Output stable JSON for programmatic callers.
        #[arg(long)]
        json: bool,
    },
    /// v0.24 Agent Inbox: run Code & Notebook Analyst against a
    /// research repo (Jupyter `.ipynb`, Python / R / Julia / Quarto
    /// / Rmd scripts). Each analysis, code-derived finding, or
    /// experiment intent becomes a `finding.add` `StateProposal`
    /// tagged with the analyst's `AgentRun`. Same review loop.
    CompileCode {
        /// Repo / folder root to walk.
        root: PathBuf,
        /// Frontier file the proposals are appended to.
        #[arg(long)]
        frontier: PathBuf,
        /// Optional model alias (`sonnet`, `opus`, …).
        #[arg(short, long)]
        backend: Option<String>,
        /// Cap on files processed (default 30).
        #[arg(long)]
        max_files: Option<usize>,
        /// Preview without writing to the frontier file.
        #[arg(long)]
        dry_run: bool,
        /// Output stable JSON for programmatic callers.
        #[arg(long)]
        json: bool,
    },
    /// v0.28 Agent Inbox: run Reviewer Agent against a frontier's
    /// pending proposals. Each scored proposal gets a
    /// `finding.note` proposal attached with plausibility +
    /// evidence + scope + duplicate-risk scores so reviewers can
    /// triage faster.
    ReviewPending {
        #[arg(long)]
        frontier: PathBuf,
        #[arg(short, long)]
        backend: Option<String>,
        #[arg(long)]
        max_proposals: Option<usize>,
        /// Number of proposals scored per `claude -p` call.
        /// 1 = per-proposal mode (full transcript). 5–10 = ~5×
        /// faster wall-clock, single response covers the batch.
        /// Capped at 12 internally.
        #[arg(long, default_value = "1")]
        batch_size: usize,
        #[arg(long)]
        dry_run: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.28 Agent Inbox: run Contradiction Finder against a
    /// frontier's findings. Pairs that contradict get emitted as
    /// `tension`-typed `finding.add` proposals.
    FindTensions {
        #[arg(long)]
        frontier: PathBuf,
        #[arg(short, long)]
        backend: Option<String>,
        #[arg(long)]
        max_findings: Option<usize>,
        #[arg(long)]
        dry_run: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.28 Agent Inbox: run Experiment Planner against a
    /// frontier's open questions and hypotheses. Each gets 1–3
    /// `experiment_intent`-typed `finding.add` proposals.
    PlanExperiments {
        #[arg(long)]
        frontier: PathBuf,
        #[arg(short, long)]
        backend: Option<String>,
        #[arg(long)]
        max_findings: Option<usize>,
        #[arg(long)]
        dry_run: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.25 Agent Inbox: run Datasets agent against a folder of
    /// CSV / TSV files. Each dataset gets a summary
    /// proposal + optional supported-claim proposals tagged with
    /// the agent's `AgentRun`. Same review loop.
    CompileData {
        /// Folder root to walk (top level only in v0.25).
        root: PathBuf,
        /// Frontier file the proposals are appended to.
        #[arg(long)]
        frontier: PathBuf,
        /// Optional model alias (`sonnet`, `opus`, …).
        #[arg(short, long)]
        backend: Option<String>,
        /// Sample rows sent to the model per dataset (default 50).
        #[arg(long)]
        sample_rows: Option<usize>,
        /// Preview without writing to the frontier file.
        #[arg(long)]
        dry_run: bool,
        /// Output stable JSON for programmatic callers.
        #[arg(long)]
        json: bool,
    },
    /// Check frontier quality and proof readiness
    Check {
        /// Frontier JSON file, Vela repo, or proof packet
        source: Option<PathBuf>,
        /// Run schema validation
        #[arg(long)]
        schema: bool,
        /// Run frontier lint checks
        #[arg(long)]
        stats: bool,
        /// Run conformance vectors
        #[arg(long)]
        conformance: bool,
        /// Conformance test directory
        #[arg(long, default_value = "tests/conformance")]
        conformance_dir: PathBuf,
        /// Run all checks
        #[arg(long)]
        all: bool,
        /// Run only structural schema validation
        #[arg(long)]
        schema_only: bool,
        /// Treat warnings and blocking signals as failures
        #[arg(long)]
        strict: bool,
        /// Show fix suggestions
        #[arg(long)]
        fix: bool,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
    },
    /// Check structural integrity of accepted frontier state
    Integrity {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
    },
    /// Report downstream impact for one finding without mutating state
    Impact {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Finding id to inspect
        finding_id: String,
        /// Maximum dependency depth
        #[arg(long)]
        depth: Option<usize>,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
    },
    /// v0.95: Aggregate discord report across every finding in the
    /// frontier. Runs the v0.83 detectors (`evidence_gap`,
    /// `provenance_fragile`, `status_divergent`) over the live event
    /// log and reports the support set. Useful for surfacing
    /// retraction-fragile claims, missing-evidence findings, and
    /// drift between on-disk flags and substrate-derived BelnapStatus.
    Discord {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
        /// Filter to a single discord kind (e.g.
        /// `provenance_fragile`, `evidence_gap`, `status_divergent`).
        /// When omitted, all kinds are included.
        #[arg(long)]
        kind: Option<String>,
    },
    /// Normalize deterministic frontier state without changing claims
    Normalize {
        /// Frontier JSON file or Vela repo
        source: PathBuf,
        /// Output normalized frontier copy
        #[arg(short, long)]
        out: Option<PathBuf>,
        /// Write changes back to the input
        #[arg(long)]
        write: bool,
        /// Force dry-run
        #[arg(long)]
        dry_run: bool,
        /// Rewrite finding IDs to content addresses and update links
        #[arg(long)]
        rewrite_ids: bool,
        /// Write old-to-new ID map when rewriting IDs
        #[arg(long)]
        id_map: Option<PathBuf>,
        /// Phase N: regenerate finding.provenance fields (title, year,
        /// journal, authors, license, publisher, funders) from the
        /// canonical SourceRecord matched by DOI / PMID / title.
        #[arg(long)]
        resync_provenance: bool,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
    },
    /// Export and validate a proof packet
    Proof {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Output proof packet directory
        #[arg(long, short = 'o', default_value = "proof-packet")]
        out: PathBuf,
        /// Proof packet template
        #[arg(long, default_value = "bbb-alzheimer")]
        template: String,
        /// Optional benchmark suite to include
        #[arg(long)]
        gold: Option<PathBuf>,
        /// Record latest proof packet state back into the input frontier
        #[arg(long)]
        record_proof_state: bool,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
    },
    /// Inspect a split frontier repository as a state machine
    Repo {
        #[command(subcommand)]
        action: RepoAction,
    },
    /// Serve a read-only frontier over MCP stdio or HTTP
    Serve {
        /// Frontier JSON file or Vela repo
        #[arg(required_unless_present_any = ["frontiers", "setup"])]
        frontier: Option<PathBuf>,
        /// Directory of frontier files
        #[arg(long)]
        frontiers: Option<PathBuf>,
        /// LLM backend reserved for future optional tools
        #[arg(short, long)]
        backend: Option<String>,
        /// Run an HTTP server on this port instead of MCP stdio
        #[arg(long)]
        http: Option<u16>,
        /// Print MCP setup instructions
        #[arg(long)]
        setup: bool,
        /// Validate public tool contracts and exit
        #[arg(long)]
        check_tools: bool,
        /// Output stable JSON for --check-tools
        #[arg(long)]
        json: bool,
        /// Serve the local Workbench web UI (`web/`) alongside the
        /// HTTP API. Implies `--http` if no port is specified
        /// (default 3848). Phase R, v0.5.
        #[arg(long)]
        workbench: bool,
    },
    /// v0.42: Show what's pending right now — the daily-driver
    /// equivalent of `git status`. One screen: counts, the inbox,
    /// the audit, the federation health. Read in two seconds.
    Status {
        frontier: PathBuf,
        /// Output stable JSON for programmatic callers.
        #[arg(long)]
        json: bool,
    },
    /// v0.42: Recent canonical events in human-readable form. The
    /// `git log` analogue. Default newest-first; cap on count.
    Log {
        frontier: PathBuf,
        /// How many recent events to show.
        #[arg(long, default_value = "20")]
        limit: usize,
        /// Filter to events matching this kind (substring match).
        #[arg(long)]
        kind: Option<String>,
        /// Output stable JSON.
        #[arg(long)]
        json: bool,
    },
    /// v0.42: Triage list of pending proposals. What you sit down to
    /// review. Reviewer-agent scores surface where present; flagged
    /// items rise to the top.
    Inbox {
        frontier: PathBuf,
        /// Show only proposals matching this kind (substring match).
        #[arg(long)]
        kind: Option<String>,
        /// Cap on entries shown.
        #[arg(long, default_value = "30")]
        limit: usize,
        /// Output stable JSON.
        #[arg(long)]
        json: bool,
    },
    /// v0.42: Conversational substrate access. Type a natural-language
    /// question; the substrate routes it to a structured query and
    /// renders the answer. No agent in the loop — kernel queries only.
    /// Codex-flavored REPL that doesn't pretend to be an agent.
    Ask {
        frontier: PathBuf,
        /// The question. If omitted, drops into a REPL.
        #[arg(trailing_var_arg = true)]
        question: Vec<String>,
        /// Output stable JSON when the answer has structure.
        #[arg(long)]
        json: bool,
    },
    /// Show frontier statistics
    Stats {
        /// Frontier JSON file, Vela repo, or packet
        frontier: PathBuf,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
    },
    /// Search findings
    Search {
        /// Search query
        query: String,
        /// Frontier JSON file, Vela repo, or packet
        #[arg(long)]
        source: Option<PathBuf>,
        /// Filter by entity
        #[arg(long)]
        entity: Option<String>,
        /// Filter by assertion type
        #[arg(long)]
        r#type: Option<String>,
        /// Search every frontier in a directory
        #[arg(long)]
        all: Option<PathBuf>,
        /// Maximum results
        #[arg(long, default_value = "20")]
        limit: usize,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
    },
    /// List candidate contradictions and tensions
    Tensions {
        source: PathBuf,
        #[arg(long)]
        both_high: bool,
        #[arg(long)]
        cross_domain: bool,
        #[arg(long, default_value = "20")]
        top: usize,
        #[arg(long)]
        json: bool,
    },
    /// Inspect and rank candidate gap review leads
    Gaps {
        #[command(subcommand)]
        action: GapsAction,
    },
    /// Find candidate cross-domain connections
    Bridge {
        /// Input frontier JSON files or Vela repos
        #[arg(required = true)]
        inputs: Vec<PathBuf>,
        /// Run rough PubMed prior-art checks for top bridges
        #[arg(long, default_value = "true", action = clap::ArgAction::Set)]
        novelty: bool,
        /// Max bridges to check
        #[arg(long, default_value = "30")]
        top: usize,
    },
    /// Export frontier artifacts
    Export {
        frontier: PathBuf,
        #[arg(short, long, default_value = "csv")]
        format: String,
        #[arg(short, long)]
        output: Option<PathBuf>,
    },
    /// Inspect or validate proof packets
    Packet {
        #[command(subcommand)]
        action: PacketAction,
    },
    /// Recompute SHA-256 over every file in a proof packet, compare to
    /// the manifest, and validate the proof-trace chain. Friendlier
    /// alias for `vela packet validate <path>` — same code path, same
    /// guarantee. Use this when you've pulled a packet from someone
    /// else and want one command that says "yes, this is what they
    /// signed, byte for byte."
    Verify {
        /// Path to the proof packet directory (the one with manifest.json)
        path: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Run deterministic benchmark gates.
    ///
    /// Two modes:
    ///   - **legacy** (extraction quality): `--gold <gold.json>`
    ///     against an extracted-findings frontier. Pre-v0.26
    ///     behaviour, unchanged.
    ///   - **v0.26 VelaBench** (agent state-update scoring): pass
    ///     `--candidate <frontier.json>` together with `--gold`
    ///     to compare a candidate frontier (typically agent-
    ///     generated) against a curator-validated gold. Composite
    ///     score with optional `--threshold` for CI gating.
    Bench {
        /// Frontier file for single-task benchmark (legacy mode).
        frontier: Option<PathBuf>,
        /// Gold frontier (used by both modes).
        #[arg(long)]
        gold: Option<PathBuf>,
        /// v0.26: Candidate frontier to score against `--gold`.
        /// Presence of this flag selects VelaBench (agent state-
        /// update scoring) instead of the legacy extraction harness.
        #[arg(long)]
        candidate: Option<PathBuf>,
        /// v0.26: Optional source-files directory for
        /// `evidence_fidelity` checks. Without it, that metric is
        /// dropped from the composite (weights rebalanced).
        #[arg(long)]
        sources: Option<PathBuf>,
        /// v0.26: Composite-score threshold; non-zero exit if
        /// composite < threshold. Default 0.0 (report only).
        #[arg(long)]
        threshold: Option<f64>,
        /// v0.26: Write the JSON report to this path in addition
        /// to printing.
        #[arg(long)]
        report: Option<PathBuf>,
        #[arg(long)]
        entity_gold: Option<PathBuf>,
        #[arg(long)]
        link_gold: Option<PathBuf>,
        #[arg(long)]
        suite: Option<PathBuf>,
        #[arg(long)]
        suite_ready: bool,
        #[arg(long)]
        min_f1: Option<f64>,
        #[arg(long)]
        min_precision: Option<f64>,
        #[arg(long)]
        min_recall: Option<f64>,
        #[arg(long)]
        no_thresholds: bool,
        #[arg(long)]
        json: bool,
    },
    /// Run protocol conformance vectors
    Conformance {
        #[arg(default_value = "tests/conformance")]
        dir: PathBuf,
    },
    /// Show version information
    Version,
    /// Optional signing and signature verification
    Sign {
        #[command(subcommand)]
        action: SignAction,
    },
    /// Manage the frontier's registered actor identities (Phase M, v0.4)
    Actor {
        #[command(subcommand)]
        action: ActorAction,
    },
    /// v0.39: Manage the frontier's federation peer registry. A peer
    /// is another hub this frontier knows about — id, HTTPS URL, and
    /// the Ed25519 pubkey they sign manifests with. Adding a peer
    /// declares awareness; the actual sync runtime ships in v0.39.1+.
    Federation {
        #[command(subcommand)]
        action: FederationAction,
    },
    /// v0.40: Causal reasoning over the schema landed in v0.38. Audits
    /// every finding for identifiability: does the declared
    /// study-design grade actually support the causal claim being
    /// made? Surfaces underidentified findings (intervention from
    /// observational) and conditional ones (intervention from
    /// quasi-experimental designs that need explicit assumptions).
    Causal {
        #[command(subcommand)]
        action: CausalAction,
    },
    /// Manage frontier-level metadata: cross-frontier dependencies (v0.8).
    /// Use `vela frontier add-dep` to declare a remote frontier this
    /// frontier links into via `vf_…@vfr_…` references.
    Frontier {
        #[command(subcommand)]
        action: FrontierAction,
    },
    /// Walk the local Workbench draft queue (Phase R, v0.5):
    /// list, sign-and-apply, or clear queued review actions
    Queue {
        #[command(subcommand)]
        action: QueueAction,
    },
    /// Publish, list, or pull frontiers through a registry
    /// (Phase S, v0.5: verifiable distribution)
    Registry {
        #[command(subcommand)]
        action: RegistryAction,
    },
    /// Initialize a .vela frontier repo
    Init {
        #[arg(default_value = ".")]
        path: PathBuf,
        #[arg(long, default_value = "unnamed")]
        name: String,
        #[arg(long, default_value = "default")]
        template: String,
        #[arg(long)]
        no_git: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.103: scaffold a fresh frontier end-to-end in one command.
    /// Composes init + sign generate-keypair + actor add + finding add
    /// + a print-ready next-steps banner. Designed for the
    /// fresh-from-`cargo install` user who wants to feel the substrate
    /// in 30 seconds without memorizing the demo sequence.
    Quickstart {
        /// Frontier directory to create. Defaults to ./demo
        #[arg(default_value = "demo")]
        path: PathBuf,
        /// Frontier display name. Defaults to "Quickstart frontier".
        #[arg(long, default_value = "Quickstart frontier")]
        name: String,
        /// Reviewer / actor id under which the first finding lands.
        /// Defaults to `reviewer:you`. Override with e.g.
        /// `--reviewer reviewer:will-blair`.
        #[arg(long, default_value = "reviewer:you")]
        reviewer: String,
        /// First-finding assertion text. Defaults to a generic placeholder.
        /// Override with `--assertion "your real claim"`.
        #[arg(long)]
        assertion: Option<String>,
        /// Where to drop the generated keypair. Defaults to
        /// `<path>/keys/`.
        #[arg(long)]
        keys_out: Option<PathBuf>,
        /// Output stable JSON instead of the human-readable banner.
        #[arg(long)]
        json: bool,
    },
    /// v0.109: regenerate or verify the frontier's `vela.lock`
    /// pinning every cross-frontier dependency by snapshot hash.
    /// The lockfile is the substrate's "I used this exact
    /// scientific state" artifact. Default mode regenerates the
    /// lock from current state; `--check` verifies on-disk state
    /// matches the recorded lock and exits non-zero on drift.
    Lock {
        /// Frontier path (the .vela/ repo root)
        path: PathBuf,
        /// Verify the existing lock against current on-disk
        /// state instead of regenerating.
        #[arg(long)]
        check: bool,
        /// Emit JSON to stdout instead of the human banner.
        #[arg(long)]
        json: bool,
    },
    /// v0.110: generate a static HTML site documenting the
    /// frontier. Self-contained: no JS framework, no external
    /// dependencies, browseable from disk in any browser.
    /// Cargo's docs.rs analog for scientific state. Renders
    /// index, findings table, events table, and per-finding
    /// detail pages.
    Doc {
        /// Frontier path (the .vela/ repo root)
        path: PathBuf,
        /// Output directory. Defaults to `<path>/doc/`.
        #[arg(long)]
        out: Option<PathBuf>,
        /// Emit a JSON report to stdout instead of the human
        /// banner. The HTML files are written either way.
        #[arg(long)]
        json: bool,
    },
    /// Import frontier JSON into a .vela repo
    Import {
        frontier: PathBuf,
        #[arg(long)]
        into: Option<PathBuf>,
    },
    /// Compare two frontiers, or preview one pending proposal
    /// against the current frontier.
    ///
    /// v0.74: when the first positional arg starts with `vpr_`,
    /// route to the existing `proposals preview` path so a single
    /// `vela diff <proposal_id>` shows the proposal-vs-frontier
    /// delta the README quotes. The two-arg form
    /// (`vela diff <frontier_a> <frontier_b>`) keeps its existing
    /// behavior.
    Diff {
        /// Frontier path A, or a `vpr_*` proposal id for
        /// preview mode.
        target: String,
        /// Frontier path B for two-frontier compare. Omit when
        /// `target` is a proposal id.
        frontier_b: Option<PathBuf>,
        /// Frontier root for proposal-preview mode. Defaults to
        /// `.` if the first positional is a proposal id and no
        /// `--frontier` flag is provided.
        #[arg(long)]
        frontier: Option<PathBuf>,
        /// Reviewer attribution for the proposal-preview mode.
        #[arg(long, default_value = "reviewer:preview")]
        reviewer: String,
        #[arg(long)]
        json: bool,
        #[arg(long)]
        quiet: bool,
    },
    /// Inspect or apply proposal-first frontier writes
    Proposals {
        #[command(subcommand)]
        action: ProposalAction,
    },
    /// Import a Carina artifact packet as reviewable frontier proposals
    ArtifactToState {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Artifact packet JSON
        packet: PathBuf,
        /// Actor importing the packet
        #[arg(long)]
        actor: String,
        /// Apply artifact proposals immediately while leaving truth changes pending
        #[arg(long)]
        apply_artifacts: bool,
        #[arg(long)]
        json: bool,
    },
    /// Validate Carina artifact packets before importing runtime output
    BridgeKit {
        #[command(subcommand)]
        action: BridgeKitAction,
    },
    /// Run reviewed source adapters into artifact-to-state proposals
    SourceAdapter {
        #[command(subcommand)]
        action: SourceAdapterAction,
    },
    /// Run external runtime adapters into artifact-to-state proposals
    RuntimeAdapter {
        #[command(subcommand)]
        action: RuntimeAdapterAction,
    },
    /// Manage finding bundles as the core frontier primitive
    Finding {
        #[command(subcommand)]
        command: FindingCommands,
    },
    /// Add typed links between findings — including cross-frontier
    /// references of the form `vf_<id>@vfr_<id>` (v0.8). Until v0.9
    /// link state lived only in JSON; `vela link add` is the CLI on-ramp.
    Link {
        #[command(subcommand)]
        action: LinkAction,
    },
    /// v0.48: launch the local workbench web app — a localhost UI
    /// rendering the substrate against the cwd's `.vela/` repo.
    /// Read+write: confirm/refute bridges, browse findings, audit.
    /// Pure Rust, no node/bun dependency, single binary.
    Workbench {
        /// Path to a Vela repo. Defaults to cwd.
        #[arg(default_value = ".")]
        path: PathBuf,
        /// Port to bind on localhost. Default 3850.
        #[arg(long, default_value_t = 3850)]
        port: u16,
        /// Skip auto-opening the default browser.
        #[arg(long)]
        no_open: bool,
    },
    /// v0.46: derive, list, and review cross-frontier bridges.
    /// A bridge is a content-addressed `vbr_<id>` record asserting
    /// "this entity links findings in two frontiers." Bridges are
    /// derived deterministically; reviewer judgment promotes them
    /// from `derived` to `confirmed` or `refuted`.
    Bridges {
        #[command(subcommand)]
        action: BridgesAction,
    },
    /// v0.19: resolve unresolved entities against a bundled common-entity
    /// table (UniProt for proteins, MeSH for diseases, ChEBI/DrugBank for
    /// compounds, etc.). Lowers `needs_review` for matched entities and
    /// populates `canonical_id`. Idempotent unless `--force` is passed.
    Entity {
        #[command(subcommand)]
        action: EntityAction,
    },
    /// Create or apply one proposal-backed finding review
    Review {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Finding ID to review
        finding_id: String,
        /// accepted, contested, needs_revision, or rejected
        #[arg(long)]
        status: Option<String>,
        /// Reason for the review
        #[arg(long)]
        reason: Option<String>,
        /// Reviewer identifier
        #[arg(long)]
        reviewer: String,
        /// Immediately accept and apply the proposal locally
        #[arg(long)]
        apply: bool,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
    },
    /// Add a lightweight note to a finding
    Note {
        frontier: PathBuf,
        finding_id: String,
        #[arg(long)]
        text: String,
        #[arg(long)]
        author: String,
        /// Immediately accept and apply the proposal locally
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },
    /// Add an explicit caveat to a finding
    Caveat {
        frontier: PathBuf,
        finding_id: String,
        #[arg(long)]
        text: String,
        #[arg(long)]
        author: String,
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },
    /// Revise an interpretation field while preserving history
    Revise {
        frontier: PathBuf,
        finding_id: String,
        /// New confidence score from 0.0 to 1.0
        #[arg(long)]
        confidence: f64,
        /// Reason for the revision
        #[arg(long)]
        reason: String,
        /// Reviewer identifier
        #[arg(long)]
        reviewer: String,
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },
    /// Mark a finding as rejected without deleting it
    Reject {
        frontier: PathBuf,
        finding_id: String,
        #[arg(long)]
        reason: String,
        #[arg(long)]
        reviewer: String,
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },
    /// Show state-transition history for one finding
    History {
        frontier: PathBuf,
        finding_id: String,
        #[arg(long)]
        json: bool,
        /// v0.55: time-travel replay — show only events at-or-before
        /// this RFC3339 timestamp, and report the confidence score
        /// the finding had at that moment (last revision <= cutoff).
        #[arg(long, value_name = "RFC3339_TIMESTAMP")]
        as_of: Option<String>,
    },
    /// Import review/state events from a packet or JSON file into a frontier
    ImportEvents {
        source: PathBuf,
        #[arg(long)]
        into: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Retract a finding
    Retract {
        source: PathBuf,
        finding_id: String,
        #[arg(long)]
        reason: String,
        #[arg(long)]
        reviewer: String,
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.79: Add a new entity tag to an existing finding.
    /// Append-only: re-applying with the same name is a no-op.
    /// Closes the v0.78.4 honest gap that forced reviewers to
    /// append new findings just to add a tag.
    EntityAdd {
        frontier: PathBuf,
        finding_id: String,
        #[arg(long)]
        entity: String,
        /// Entity type. One of: gene, protein, compound, disease,
        /// cell_type, organism, pathway, assay, anatomical_structure,
        /// particle, instrument, dataset, quantity, other.
        #[arg(long)]
        entity_type: String,
        #[arg(long)]
        reviewer: String,
        #[arg(long)]
        reason: String,
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.57: Resolve a named entity inside a finding's
    /// assertion.entities to a canonical id. Clears the entity's
    /// needs_review flag.
    EntityResolve {
        frontier: PathBuf,
        finding_id: String,
        #[arg(long)]
        entity: String,
        #[arg(long)]
        source: String,
        #[arg(long)]
        id: String,
        #[arg(long)]
        confidence: f64,
        #[arg(long)]
        matched_name: Option<String>,
        #[arg(long, default_value = "manual")]
        resolution_method: String,
        #[arg(long)]
        reviewer: String,
        #[arg(long)]
        reason: String,
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.57: Mechanically repair a missing evidence-span on a
    /// finding by appending a `{section, text}` span. Emits a signed
    /// v0.57: Fetch metadata + abstract for an external source by
    /// stable identifier (doi:, pmid:, nct:). Cached locally so a
    /// rerun doesn't hit the network. Used by the BBB span-repair
    /// curation wave to propose evidence_spans from fetched
    /// abstract text.
    SourceFetch {
        /// Source identifier. Accepts `doi:<doi>`, `pmid:<id>`,
        /// `nct:<id>`, or a bare DOI / PMID / NCT id.
        identifier: String,
        /// Frontier to use as the cache root. If set, fetched
        /// records are cached under
        /// `<frontier>/sources/cache/<sha256>.json` and reused.
        #[arg(long)]
        cache: Option<PathBuf>,
        /// Where to write the JSON output. Defaults to stdout.
        #[arg(long)]
        out: Option<PathBuf>,
        /// Force a network fetch even if a cache hit exists.
        #[arg(long)]
        refresh: bool,
        #[arg(long)]
        json: bool,
    },
    /// `finding.span_repaired` canonical event when `--apply` is
    /// passed.
    SpanRepair {
        frontier: PathBuf,
        finding_id: String,
        #[arg(long)]
        section: String,
        #[arg(long)]
        text: String,
        #[arg(long)]
        reviewer: String,
        #[arg(long)]
        reason: String,
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.56: Mechanically repair a missing evidence-atom locator by
    /// copying the locator from the parent source record. Emits a
    /// signed `evidence_atom.locator_repaired` canonical event when
    /// `--apply` is passed.
    LocatorRepair {
        frontier: PathBuf,
        atom_id: String,
        /// Resolved locator string (e.g. doi:10.1038/s41586-020-2247-3).
        /// If omitted, the CLI looks up the parent source's locator.
        #[arg(long)]
        locator: Option<String>,
        /// Reviewer identifier (e.g. agent:vela-curation-bot or
        /// reviewer:will-blair).
        #[arg(long)]
        reviewer: String,
        /// Reason for the repair, recorded on the canonical event.
        #[arg(long)]
        reason: String,
        /// Immediately accept and apply the proposal locally.
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },
    /// Simulate correction impact over declared dependency links
    Propagate {
        frontier: PathBuf,
        #[arg(long)]
        retract: Option<String>,
        #[arg(long)]
        reduce_confidence: Option<String>,
        #[arg(long)]
        to: Option<f64>,
        #[arg(short, long)]
        output: Option<PathBuf>,
    },
    /// v0.32: Record an independent replication attempt against a
    /// canonical finding. Each attempt becomes a `vrep_<hash>` object
    /// in `.vela/replications/`, content-addressed by target +
    /// attempting actor + canonical conditions + outcome. Replication
    /// is the empirical bedrock of science; making it kernel-level
    /// means downstream tools (site, bench, agents) can reason about
    /// "this lab tried in human iPSC, that lab failed in mouse OPCs"
    /// as distinct epistemic facts.
    Replicate {
        /// Path to the frontier (project dir, `.vela/` repo, or `.json`).
        frontier: PathBuf,
        /// Target finding id (`vf_<hash>`) being replicated.
        target: String,
        /// Outcome label: `replicated` | `failed` | `partial` | `inconclusive`.
        #[arg(long)]
        outcome: String,
        /// Stable actor id of the lab/curator/agent attempting.
        #[arg(long)]
        by: String,
        /// One-paragraph description of conditions (model system,
        /// species, sample size, in_vivo / in_vitro / human_data).
        /// Goes into the content-address preimage.
        #[arg(long)]
        conditions: String,
        /// Source paper title for the replicating work.
        #[arg(long)]
        source_title: String,
        /// Optional DOI for the replicating paper.
        #[arg(long)]
        doi: Option<String>,
        /// Optional PMID for the replicating paper.
        #[arg(long)]
        pmid: Option<String>,
        /// Sample size description (e.g. "n=42").
        #[arg(long)]
        sample_size: Option<String>,
        /// Free-text reviewer note. Especially important for
        /// `partial` and `inconclusive` outcomes.
        #[arg(long, default_value = "")]
        note: String,
        /// `vrep_<id>` of a previous attempt this one extends/refines.
        #[arg(long)]
        previous_attempt: Option<String>,
        /// v0.36.2: skip the propagation cascade. By default,
        /// recording a replication recomputes the target finding's
        /// confidence from the live `Project.replications` collection
        /// and flags downstream dependents linked via `supports` /
        /// `depends`. Use this flag to stage replications without
        /// immediate review-queue churn.
        #[arg(long, default_value_t = false)]
        no_cascade: bool,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.32: List replication attempts in a frontier, optionally
    /// filtered by target finding id.
    Replications {
        /// Path to the frontier (project dir, `.vela/` repo, or `.json`).
        frontier: PathBuf,
        /// Optional target finding id to filter by.
        #[arg(long)]
        target: Option<String>,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.33: Register a Dataset as a first-class kernel object
    /// (`vd_<hash>`). Datasets anchor empirical claims that rest on
    /// data — the canonical Alzheimer's frontier should know that
    /// "ATV:TREM2 reduces plaque density" rests on a specific cohort
    /// of n=24 iPSC-derived microglia, not on "the iPSC dataset" in
    /// the abstract.
    DatasetAdd {
        /// Path to the frontier (project dir, `.vela/` repo, or `.json`).
        frontier: PathBuf,
        /// Human-readable dataset name (e.g. `ADNI`, `TRAILBLAZER-ALZ`).
        #[arg(long)]
        name: String,
        /// Semantic version or release tag (e.g. `ADNI-3`, `v2.2`).
        #[arg(long)]
        version: Option<String>,
        /// SHA-256 of canonical contents. For remote datasets, the
        /// publisher's declared content hash; integrity verification
        /// is the puller's responsibility.
        #[arg(long)]
        content_hash: String,
        /// Where the dataset is reachable (https / file / s3 URL).
        #[arg(long)]
        url: Option<String>,
        /// License identifier or URL.
        #[arg(long)]
        license: Option<String>,
        /// Source paper title or release name (for provenance).
        #[arg(long)]
        source_title: String,
        /// Optional DOI for the source publication.
        #[arg(long)]
        doi: Option<String>,
        /// Optional row count.
        #[arg(long)]
        row_count: Option<u64>,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.33: List datasets in a frontier.
    Datasets {
        frontier: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// v0.33: Register a CodeArtifact as a first-class kernel object
    /// (`vc_<hash>`). Claims can reference the code that produced
    /// them, pinned to a specific git commit and path.
    CodeAdd {
        /// Path to the frontier.
        frontier: PathBuf,
        /// Source language: `python`, `r`, `julia`, `rust`, `bash`, etc.
        #[arg(long)]
        language: String,
        /// Repository URL (e.g. `https://github.com/vela-science/vela`).
        #[arg(long)]
        repo_url: Option<String>,
        /// Specific git commit SHA. Required for reproducibility;
        /// `None` means "unpinned" and weakens the substrate claim.
        #[arg(long)]
        commit: Option<String>,
        /// Path within the repository.
        #[arg(long)]
        path: String,
        /// SHA-256 of the snippet body.
        #[arg(long)]
        content_hash: String,
        /// Optional starting line.
        #[arg(long)]
        line_start: Option<u32>,
        /// Optional ending line.
        #[arg(long)]
        line_end: Option<u32>,
        /// Optional entry point: function name, notebook cell id.
        #[arg(long)]
        entry_point: Option<String>,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.33: List code artifacts in a frontier.
    CodeArtifacts {
        frontier: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Register a generic content-addressed artifact. Use this for
    /// protocols, trial records, supplements, notebooks, source files,
    /// tables, and dataset manifests that need durable byte or pointer
    /// provenance.
    ArtifactAdd {
        /// Path to the frontier.
        frontier: PathBuf,
        /// Artifact kind. Examples: clinical_trial_record, protocol,
        /// supplement, notebook, source_file, dataset.
        #[arg(long)]
        kind: String,
        /// Human-readable artifact name.
        #[arg(long)]
        name: String,
        /// Local file to hash and, for .vela repos, mirror under
        /// `.vela/artifact-blobs/sha256/`.
        #[arg(long)]
        file: Option<PathBuf>,
        /// Remote URL or accession locator.
        #[arg(long)]
        url: Option<String>,
        /// SHA-256 commitment. Required unless `--file` is provided.
        #[arg(long)]
        content_hash: Option<String>,
        /// MIME type or close equivalent.
        #[arg(long)]
        media_type: Option<String>,
        /// License identifier, URL, or access terms note.
        #[arg(long)]
        license: Option<String>,
        /// Source title for artifact provenance. Defaults to `--name`.
        #[arg(long)]
        source_title: Option<String>,
        /// Source URL when distinct from `--url`.
        #[arg(long)]
        source_url: Option<String>,
        /// Optional DOI for the source publication.
        #[arg(long)]
        doi: Option<String>,
        /// Target finding ids this artifact bears on.
        #[arg(long)]
        target: Vec<String>,
        /// Structured metadata as key=value. Repeatable.
        #[arg(long)]
        metadata: Vec<String>,
        /// Access tier: public, restricted, or classified.
        #[arg(long, default_value = "public")]
        access_tier: String,
        /// Stable actor id of the depositor.
        #[arg(long, default_value = "reviewer:manual")]
        deposited_by: String,
        /// Reason recorded on the canonical event.
        #[arg(long, default_value = "artifact deposit")]
        reason: String,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// List generic artifacts in a frontier.
    Artifacts {
        frontier: PathBuf,
        /// Optional target finding id to filter by.
        #[arg(long)]
        target: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// Audit artifact locators, hashes, references, and profile fields.
    ArtifactAudit {
        frontier: PathBuf,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// Show the validated decision brief projection for a frontier.
    DecisionBrief {
        frontier: PathBuf,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// Show the validated trial outcome projection for a frontier.
    TrialSummary {
        frontier: PathBuf,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// Show the validated source verification projection for a frontier.
    SourceVerification {
        frontier: PathBuf,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// Show the validated source ingest plan for a frontier.
    SourceIngestPlan {
        frontier: PathBuf,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// Import a ClinicalTrials.gov v2 study record as a content-addressed
    /// `clinical_trial_record` artifact.
    ClinicalTrialImport {
        /// Path to the frontier.
        frontier: PathBuf,
        /// ClinicalTrials.gov NCT identifier.
        nct_id: String,
        /// Read a saved ClinicalTrials.gov v2 JSON record instead of
        /// fetching from the network.
        #[arg(long)]
        input_json: Option<PathBuf>,
        /// Target finding ids this trial record bears on.
        #[arg(long)]
        target: Vec<String>,
        /// Stable actor id of the depositor.
        #[arg(long, default_value = "reviewer:manual")]
        deposited_by: String,
        /// Reason recorded on the canonical event.
        #[arg(long, default_value = "clinical trial record import")]
        reason: String,
        /// License or access terms note.
        #[arg(long, default_value = "ClinicalTrials.gov public record")]
        license: String,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.49: Deposit a NegativeResult (`vnr_<hash>`). Two flavors:
    /// `--kind registered_trial` for pre-registered trial readouts
    /// (carries `power`, `effect_size_ci`, and pre-registered MCID
    /// so an underpowered null does not poison downstream confidence);
    /// `--kind exploratory` for wet-lab dead ends (the
    /// (reagent, observation, attempts) tuple where most failures
    /// cannot be statistically bounded).
    NegativeResultAdd {
        /// Path to the frontier (project dir, `.vela/` repo, or `.json`).
        frontier: PathBuf,
        /// `registered_trial` or `exploratory`.
        #[arg(long)]
        kind: String,
        /// Stable actor id of the depositor.
        #[arg(long)]
        deposited_by: String,
        /// Free-text reason recorded on the canonical event.
        #[arg(long)]
        reason: String,
        /// Conditions narrative (free text). Reuses the standard
        /// `Conditions` shape; structured flags are optional.
        #[arg(long)]
        conditions_text: String,
        /// Free-text reviewer note attached to the deposit.
        #[arg(long, default_value = "")]
        notes: String,
        /// Optional `vf_*` finding ids the null bears against.
        /// Repeatable.
        #[arg(long)]
        target: Vec<String>,
        // ── registered_trial fields ──────────────────────────────
        /// Pre-specified primary endpoint
        /// (e.g. "CDR-SB change at 18 months").
        #[arg(long)]
        endpoint: Option<String>,
        /// Intervention arm description (drug + dose, etc.).
        #[arg(long)]
        intervention: Option<String>,
        /// Comparator arm description (placebo, active, SoC).
        #[arg(long)]
        comparator: Option<String>,
        /// Population scope (indication, stage, biomarker eligibility).
        #[arg(long)]
        population: Option<String>,
        /// Total participants enrolled (any arm).
        #[arg(long)]
        n_enrolled: Option<u32>,
        /// Statistical power for primary endpoint, on [0, 1].
        #[arg(long)]
        power: Option<f64>,
        /// CI lower bound for the observed primary effect size.
        #[arg(long)]
        ci_lower: Option<f64>,
        /// CI upper bound for the observed primary effect size.
        #[arg(long)]
        ci_upper: Option<f64>,
        /// Pre-registered minimum effect size of interest (MCID).
        #[arg(long)]
        effect_size_threshold: Option<f64>,
        /// Trial registry id (e.g. "NCT04532333").
        #[arg(long)]
        registry_id: Option<String>,
        // ── exploratory fields ───────────────────────────────────
        /// Reagent / compound / vector / perturbation tried.
        #[arg(long)]
        reagent: Option<String>,
        /// Free-text observed outcome.
        #[arg(long)]
        observation: Option<String>,
        /// Number of independent attempts that agreed.
        #[arg(long)]
        attempts: Option<u32>,
        // ── provenance ───────────────────────────────────────────
        /// Provenance source title (paper title, trial readout, etc.).
        #[arg(long)]
        source_title: String,
        /// Optional DOI for the source.
        #[arg(long)]
        doi: Option<String>,
        /// Optional URL for the source (registry page, preprint).
        #[arg(long)]
        url: Option<String>,
        /// Optional source year.
        #[arg(long)]
        year: Option<i32>,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.49: List NegativeResults in a frontier.
    NegativeResults {
        frontier: PathBuf,
        /// Filter to deposits bearing on a specific `vf_*` finding.
        #[arg(long)]
        target: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// v0.50: Open a Trajectory (`vtr_<hash>`) — the search path that
    /// produced (or did not produce) a finding. Steps are appended
    /// via `vela trajectory-step` so the search becomes visible as
    /// it unfolds rather than only after the fact.
    TrajectoryCreate {
        /// Path to the frontier.
        frontier: PathBuf,
        /// Stable actor id of the depositor.
        #[arg(long)]
        deposited_by: String,
        /// Free-text reason recorded on the canonical event.
        #[arg(long)]
        reason: String,
        /// Optional `vf_*` finding ids the trajectory targets.
        /// Repeatable. May be empty when the trajectory leads
        /// nowhere yet — the search can be opened before its target
        /// finding exists.
        #[arg(long)]
        target: Vec<String>,
        /// Free-text reviewer note on the trajectory as a whole.
        #[arg(long, default_value = "")]
        notes: String,
        #[arg(long)]
        json: bool,
    },
    /// v0.50: Append one step to an existing Trajectory. Steps are
    /// content-addressed and idempotent on duplicate content.
    TrajectoryStep {
        /// Path to the frontier.
        frontier: PathBuf,
        /// Trajectory `vtr_<hash>` to append to.
        trajectory_id: String,
        /// Step kind: `hypothesis | tried | ruled_out | observed | refined`.
        #[arg(long)]
        kind: String,
        /// Free-text description. For `ruled_out`, prose should name
        /// the reason for exclusion — that's the load-bearing field
        /// for the next agent reading the search.
        #[arg(long)]
        description: String,
        /// Stable actor id of who took the step.
        #[arg(long)]
        actor: String,
        /// Free-text reason recorded on the canonical event.
        #[arg(long)]
        reason: String,
        /// Optional referenced kernel objects (`vf_*`, `vnr_*`,
        /// `vrep_*`, `vpred_*`, `vd_*`, `vc_*`). Repeatable.
        #[arg(long)]
        reference: Vec<String>,
        #[arg(long)]
        json: bool,
    },
    /// v0.50: List trajectories in a frontier.
    Trajectories {
        frontier: PathBuf,
        /// Filter to trajectories bearing on a specific `vf_*` finding.
        #[arg(long)]
        target: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// v0.51: Re-classify the read-side access tier of a finding,
    /// negative_result, or trajectory. Emits a `tier.set` canonical
    /// event so the reclassification is replay-deterministic and
    /// auditable. Higher tiers are gated in MCP/HTTP read paths
    /// against the requesting actor's `access_clearance`.
    TierSet {
        /// Path to the frontier.
        frontier: PathBuf,
        /// One of `finding`, `negative_result`, `trajectory`.
        #[arg(long)]
        object_type: String,
        /// `vf_*`, `vnr_*`, or `vtr_*` id.
        #[arg(long)]
        object_id: String,
        /// New tier: `public`, `restricted`, or `classified`.
        #[arg(long)]
        tier: String,
        /// Stable actor id of the classifier (must already be
        /// registered if signed events are required by the frontier).
        #[arg(long)]
        actor: String,
        /// Free-text reason recorded on the canonical event. Often
        /// the load-bearing audit field — "why was this classified."
        #[arg(long)]
        reason: String,
        #[arg(long)]
        json: bool,
    },
    /// v0.34: Make a falsifiable Prediction (`vpred_<hash>`) about a
    /// future observation. Predictions are scoped to one or more
    /// existing findings, carry an explicit resolution criterion,
    /// and live in the kernel's epistemic accountability ledger.
    /// When a Resolution arrives later, the prediction's confidence
    /// flows into the predictor's Brier score and log score.
    Predict {
        /// Path to the frontier (project dir, `.vela/` repo, or `.json`).
        frontier: PathBuf,
        /// Stable actor id of the predictor.
        #[arg(long)]
        by: String,
        /// Plain-prose prediction (e.g. "lecanemab Phase 4 will show
        /// >0.4 SD CDR-SB effect").
        #[arg(long)]
        claim: String,
        /// Unambiguous criterion describing how to recognize resolution.
        #[arg(long)]
        criterion: String,
        /// RFC 3339 deadline for resolution.
        #[arg(long)]
        resolves_by: Option<String>,
        /// Confidence on [0, 1] in the expected outcome.
        #[arg(long)]
        confidence: f64,
        /// Comma-separated `vf_*` finding ids this prediction depends on.
        #[arg(long, default_value = "")]
        target: String,
        /// Outcome shape: `affirmed` | `falsified` | `quant:V±T units` | `cat:value`.
        #[arg(long, default_value = "affirmed")]
        outcome: String,
        /// Free-text scope/conditions of the prediction.
        #[arg(long, default_value = "")]
        conditions: String,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.34: Resolve an open Prediction. Records what actually
    /// happened, who observed it, and whether it matched the
    /// prediction. Drives Brier / log-score / hit-rate calibration
    /// over the resolved subset.
    Resolve {
        /// Path to the frontier.
        frontier: PathBuf,
        /// `vpred_<id>` of the prediction being resolved.
        prediction: String,
        /// Free-text description of what actually happened.
        #[arg(long)]
        outcome: String,
        /// Whether the actual outcome matched the predicted one.
        #[arg(long)]
        matched: bool,
        /// Stable actor id of the resolver. Independent resolvers
        /// (different from the predictor) produce stronger signal.
        #[arg(long)]
        by: String,
        /// Resolver's confidence in the match judgment, on [0, 1].
        #[arg(long, default_value = "1.0")]
        confidence: f64,
        /// Source paper / trial readout title for the resolution.
        #[arg(long, default_value = "")]
        source_title: String,
        /// Optional DOI for the resolving source.
        #[arg(long)]
        doi: Option<String>,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.34: List predictions in a frontier with their resolution state.
    Predictions {
        frontier: PathBuf,
        /// Optional actor filter.
        #[arg(long)]
        by: Option<String>,
        /// Show only unresolved predictions.
        #[arg(long)]
        open: bool,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.34: Compute calibration scores (Brier, log score, hit rate)
    /// for one or all actors with predictions in the frontier.
    Calibration {
        frontier: PathBuf,
        /// Optional actor filter (e.g. `reviewer:will-blair`).
        #[arg(long)]
        actor: Option<String>,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
    /// v0.40.1: Walk every prediction and mark as `expired_unresolved`
    /// any whose deadline has passed without an explicit Resolution.
    /// Emits one `prediction.expired_unresolved` event per newly-
    /// expired prediction. Idempotent. Calibration counts expired
    /// predictions separately from resolved ones — the predictor is
    /// answering for the missing commitment without their Brier or
    /// log score being moved by it.
    PredictionsExpire {
        frontier: PathBuf,
        /// Override the system clock (RFC 3339). Useful for tests
        /// and reproducibility; defaults to `now`.
        #[arg(long)]
        now: Option<String>,
        /// Run the check but don't write any events or flag any
        /// predictions. Reports what *would* expire.
        #[arg(long)]
        dry_run: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.35: Compute consensus over claim-similar findings, weighted
    /// by evidence quality. Takes a target `vf_<id>` and finds other
    /// findings making a similar assertion (shared entities + text
    /// overlap), weighs them by replication count + citation count
    /// + review state, and returns a consensus confidence with a
    /// credible interval. The substrate move that turns "what does
    /// the field hold about X?" from a manual graph walk into a
    /// queryable result.
    Consensus {
        /// Path to the frontier (project dir, `.vela/` repo, or `.json`).
        frontier: PathBuf,
        /// Target finding id (`vf_<hash>`).
        target: String,
        /// Weighting scheme: `unweighted` | `replication` | `citation` |
        /// `composite`. Default is `composite`.
        #[arg(long, default_value = "composite")]
        weighting: String,
        /// v0.38.2: restrict neighbor findings to a specific causal
        /// claim type: `correlation` | `mediation` | `intervention`.
        /// Useful for asking "what does the field hold *as
        /// causation*?" — distinct from the global blend.
        #[arg(long)]
        causal_claim: Option<String>,
        /// v0.38.2: restrict neighbor findings to study designs at or
        /// above the given grade: `theoretical` | `observational` |
        /// `quasi_experimental` | `rct`. Findings with no grade are
        /// excluded when this is set.
        #[arg(long)]
        causal_grade_min: Option<String>,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },

    // v0.74: top-level alias verbs. Each variant is a thin wrapper
    // routing to an existing canonical-event emission path. No new
    // substrate logic. The aliases exist so the daily flow reads
    // `init / ingest / propose / diff / accept / attest / log /
    // lineage / serve` rather than burying the verbs under
    // `proposals accept`, `sign apply`, `history`. See plan
    // v0.74.1.
    /// v0.74: ingest a single file or folder, dispatching by
    /// extension to the right backing path. Aliases:
    ///   `.pdf` or folder of pdfs -> `scout`
    ///   `.md` or folder of notes -> `compile-notes`
    ///   `.csv` / `.tsv`          -> `compile-data`
    ///   `.json` (Carina packet)  -> `artifact-to-state`
    ///   `doi:` / `pmid:` / `nct:` URI -> `source-fetch`
    ///   repo dir                 -> `compile-code`
    Ingest {
        /// File path or folder to ingest. Also accepts a stable
        /// identifier URI (`doi:<doi>`, `pmid:<id>`, `nct:<id>`).
        path: String,
        /// Frontier file or `.vela/` repo the proposals or sources
        /// land in.
        #[arg(long)]
        frontier: PathBuf,
        /// LLM backend override for agent-driven paths
        /// (scout/compile-*). Ignored for source-fetch and
        /// artifact-to-state.
        #[arg(short, long)]
        backend: Option<String>,
        /// Actor recording the ingest. Required for
        /// artifact-to-state; defaults to
        /// `agent:vela-ingest-bot` for agent paths.
        #[arg(long)]
        actor: Option<String>,
        /// Preview without writing.
        #[arg(long)]
        dry_run: bool,
        #[arg(long)]
        json: bool,
    },

    /// v0.74: shortcut for the most common reviewer proposal, a
    /// `finding.review` verdict. Mirrors `vela review`. Other
    /// proposal kinds (note, caveat, revise, reject, retract)
    /// keep their existing top-level verbs and stay reachable via
    /// `vela help advanced`.
    Propose {
        frontier: PathBuf,
        finding_id: String,
        /// One of: accepted | needs_revision | contested | rejected.
        #[arg(long)]
        status: String,
        #[arg(long)]
        reason: String,
        #[arg(long)]
        reviewer: String,
        /// Apply the proposal immediately under reviewer authority
        /// (writes a signed canonical event).
        #[arg(long)]
        apply: bool,
        #[arg(long)]
        json: bool,
    },

    /// v0.74: alias for `proposals accept`. Apply a pending
    /// proposal under the configured reviewer id, emitting the
    /// signed canonical event.
    Accept {
        frontier: PathBuf,
        proposal_id: String,
        #[arg(long)]
        reviewer: String,
        #[arg(long)]
        reason: String,
        #[arg(long)]
        json: bool,
    },

    /// v0.74: alias for `sign apply`. Sign every unsigned finding
    /// in the frontier under the supplied private key.
    ///
    /// v0.80: extended with `--event <vev_id>` for per-event
    /// attestation. When `--event` is supplied, instead of signing
    /// findings frontier-wide, the substrate emits an
    /// `attestation.recorded` canonical event pointing at the
    /// target event id. Useful for layered attestation
    /// (e.g. a second reviewer countersigning a finding.reviewed
    /// event, or a Lean run attesting a Stupp-protocol claim by
    /// pointing at its accept event).
    Attest {
        /// Frontier path. Required.
        frontier: PathBuf,
        /// Per-event mode: target event id (`vev_*`).
        /// When omitted, runs the v0.74 frontier-wide
        /// `sign apply` path.
        #[arg(long)]
        event: Option<String>,
        /// Reviewer attester id (`reviewer:<name>` or
        /// `agent:<name>`). Required for per-event mode.
        #[arg(long)]
        attester: Option<String>,
        /// Scope note explaining what this attestation covers.
        /// Required for per-event mode.
        #[arg(long)]
        scope_note: Option<String>,
        /// Optional Carina Proof primitive id (`vpf_*`) the
        /// attestation is backed by.
        #[arg(long)]
        proof_id: Option<String>,
        /// Optional Ed25519 signature over the target event's
        /// canonical preimage. Future-cycle work to verify; today
        /// the substrate stores the signature and trusts the
        /// emitter's keypair.
        #[arg(long)]
        signature: Option<String>,
        /// v0.74 frontier-wide path: private key for `sign apply`.
        /// Ignored in per-event mode.
        #[arg(long)]
        key: Option<PathBuf>,
        #[arg(long)]
        json: bool,
    },

    /// v0.74: alias for `history`. Show the state-transition replay
    /// for one finding, optionally as-of an RFC3339 timestamp.
    Lineage {
        frontier: PathBuf,
        finding_id: String,
        #[arg(long, value_name = "RFC3339_TIMESTAMP")]
        as_of: Option<String>,
        #[arg(long)]
        json: bool,
    },

    /// v0.75: validate Carina-shaped JSON against the bundled
    /// schemas, list bundled primitives, or print one schema.
    Carina {
        #[command(subcommand)]
        action: CarinaAction,
    },

    /// v0.78: Atlas-level surface. Compose multiple Vela
    /// frontiers into a domain-level living map (`vat_*`).
    /// Read-only over per-frontier event logs. See
    /// `docs/MISSION_ATLAS.md`.
    Atlas {
        #[command(subcommand)]
        action: AtlasAction,
    },

    /// v0.82: Constellation-level surface. Compose multiple
    /// Atlases into a cross-domain network (`vco_*`). The
    /// fifteenth Carina primitive's CLI surface. Read-only
    /// over per-Atlas snapshots. See `docs/MISSION_ATLAS.md`
    /// and `docs/CONSTELLATE.md`.
    Constellation {
        #[command(subcommand)]
        action: ConstellationAction,
    },
}

/// v0.78: actions on the Atlas-level surface. Each routes through
/// a handler registered by the binary at startup, calling into the
/// `vela-atlas` crate. Doctrine: read-only over per-frontier event
/// logs; never mutates frontier state.
#[derive(Subcommand)]
enum AtlasAction {
    /// Scaffold a new Atlas at `<atlases-root>/<name>/manifest.yaml`
    /// pointing at one or more existing frontier paths. Computes a
    /// content-addressed `vat_*` id from the composing frontier
    /// vfr_ids.
    Init {
        /// Atlas name (also used for the directory under
        /// `<atlases-root>/`).
        name: String,
        /// Frontier paths to compose. At least one required.
        #[arg(long, value_delimiter = ',', num_args = 1..)]
        frontiers: Vec<PathBuf>,
        /// Scientific domain (e.g. `oncology`,
        /// `additive combinatorics`).
        #[arg(long, default_value = "general")]
        domain: String,
        /// Optional bounded-question scope text.
        #[arg(long)]
        scope_note: Option<String>,
        /// Atlases root directory. Defaults to `./atlases/`.
        #[arg(long, default_value = "atlases")]
        atlases_root: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Materialize an Atlas: read each composing frontier, union
    /// accepted-core findings, compute composition hash, write
    /// `<atlases-root>/<name>/snapshot.json`.
    Materialize {
        /// Atlas name (directory under `<atlases-root>/`).
        name: String,
        #[arg(long, default_value = "atlases")]
        atlases_root: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Open the local Workbench against the Atlas-level snapshot.
    /// At v0.78 this delegates to the per-frontier Workbench for
    /// the first composing frontier; the dedicated Atlas-level
    /// Workbench page lands in v0.79+.
    Serve {
        name: String,
        #[arg(long, default_value = "atlases")]
        atlases_root: PathBuf,
        #[arg(long, default_value_t = 3848)]
        port: u16,
        #[arg(long)]
        no_open: bool,
    },
    /// v0.81.2: Update an existing Atlas by adding or removing
    /// composing frontiers. Re-computes the Atlas's `vat_*` id
    /// from the new composing-frontier list (content-addressing
    /// is honest about composition changes). Avoids the
    /// `rm -rf atlases/<name> && atlas init` workflow that the
    /// v0.78 substrate forced.
    Update {
        name: String,
        /// Frontier paths to add (idempotent: already-composed
        /// frontiers are skipped).
        #[arg(long, value_delimiter = ',')]
        add_frontier: Vec<PathBuf>,
        /// `vfr_*` ids to remove from the Atlas. Errors if any
        /// id isn't currently composed.
        #[arg(long, value_delimiter = ',')]
        remove_vfr_id: Vec<String>,
        #[arg(long, default_value = "atlases")]
        atlases_root: PathBuf,
        #[arg(long)]
        json: bool,
    },
}

/// v0.82: actions on the Constellation-level surface.
/// Mirrors AtlasAction one layer up: Atlases compose into a
/// Constellation just as frontiers compose into an Atlas.
#[derive(Subcommand)]
enum ConstellationAction {
    /// Scaffold a new Constellation pointing at one or more
    /// Atlas dirs. Computes a content-addressed `vco_*` id
    /// from the composing-atlas vat_id list.
    Init {
        name: String,
        /// Atlas directories to compose. At least one required.
        #[arg(long, value_delimiter = ',', num_args = 1..)]
        atlases: Vec<PathBuf>,
        #[arg(long)]
        scope_note: Option<String>,
        #[arg(long, default_value = "constellations")]
        constellations_root: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Materialize a Constellation: re-materialize each
    /// composing Atlas on demand, sum findings + events +
    /// bridges across, compute composition hash, write
    /// `snapshot.json` and a static `index.html`.
    Materialize {
        name: String,
        #[arg(long, default_value = "constellations")]
        constellations_root: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Serve the Constellation snapshot over HTTP. Static-file
    /// only at v0.82; interactive cross-Atlas surfaces are
    /// future cycles.
    Serve {
        name: String,
        #[arg(long, default_value = "constellations")]
        constellations_root: PathBuf,
        #[arg(long, default_value_t = 3849)]
        port: u16,
        #[arg(long)]
        no_open: bool,
    },
}

/// v0.75: actions on the Carina spec deliverable. Each one talks
/// to the schemas embedded under
/// `crates/vela-protocol/embedded/carina-schemas/`.
#[derive(Subcommand)]
enum CarinaAction {
    /// Validate a JSON file against the matching Carina schema.
    /// Detects the primitive automatically from the input's
    /// `schema: "carina.<name>.v0.X"` field, or accepts an
    /// explicit `--primitive <name>`.
    Validate {
        /// Path to a JSON file containing one Carina primitive,
        /// or a `primitives.v0.X.json`-style aggregate object
        /// with a `primitives` map.
        path: PathBuf,
        /// Override auto-detection: validate as a specific
        /// primitive (`finding`, `evidence`, `proof`, ...).
        #[arg(long)]
        primitive: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// List the 14 bundled Carina primitives.
    List {
        #[arg(long)]
        json: bool,
    },
    /// Print one bundled Carina schema to stdout.
    Schema { primitive: String },
}

#[derive(Subcommand)]
enum PacketAction {
    /// Inspect a proof packet manifest
    Inspect {
        path: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Validate a proof packet
    Validate {
        path: PathBuf,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum SignAction {
    /// Generate an Ed25519 keypair
    GenerateKeypair {
        #[arg(long, default_value = ".vela/keys")]
        out: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Sign unsigned findings in a frontier
    Apply {
        frontier: PathBuf,
        #[arg(long)]
        private_key: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Verify frontier signatures
    Verify {
        frontier: PathBuf,
        #[arg(long)]
        public_key: Option<PathBuf>,
        #[arg(long)]
        json: bool,
    },
    /// v0.37: Attach a multi-signature threshold to a finding. Once
    /// `k` distinct registered actors have each signed the finding, it
    /// is marked `jointly_accepted`. Setting `--to 1` is equivalent to
    /// the default single-sig regime.
    ThresholdSet {
        frontier: PathBuf,
        /// Target finding id (`vf_<hash>`).
        finding_id: String,
        /// Number of unique valid signatures required (>= 1).
        #[arg(long)]
        to: u32,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum ActorAction {
    /// Register an Ed25519 public key for a stable actor identity
    Add {
        frontier: PathBuf,
        /// Stable actor id (e.g. "reviewer:will-blair")
        id: String,
        /// Hex-encoded Ed25519 public key (64 hex chars)
        #[arg(long)]
        pubkey: String,
        /// Optional trust tier (Phase α, v0.6). Currently recognized:
        /// "auto-notes" — permits one-call propose_and_apply_note.
        /// Unknown tier strings load fine but never grant auto-apply.
        #[arg(long)]
        tier: Option<String>,
        /// v0.43: Optional ORCID identifier for cross-system identity.
        /// Format `0000-0000-0000-000X`. Accepts bare form, URL form
        /// (`https://orcid.org/0000-...`), or `orcid:` prefix.
        #[arg(long)]
        orcid: Option<String>,
        /// v0.51: Optional read-side access clearance.
        /// `public` (default), `restricted`, or `classified`. Higher
        /// clearance permits reading lower-tier objects through
        /// `vela serve`'s actor-aware MCP/HTTP read paths.
        #[arg(long)]
        clearance: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// List registered actors in a frontier
    List {
        frontier: PathBuf,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum CausalAction {
    /// v0.40: Audit every finding's (causal_claim, causal_evidence_grade)
    /// for identifiability. Reports underidentified, conditional,
    /// and underdetermined findings with rationale + remediation.
    Audit {
        frontier: PathBuf,
        /// Restrict the report to entries needing reviewer attention
        /// (Underidentified or Conditional). Useful for triage.
        #[arg(long)]
        problems_only: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.44 (Pearl level 2): Identify the causal effect of a source
    /// finding on a target finding by searching for a back-door
    /// adjustment set in the frontier's directed link graph. Reports
    /// either the adjustment set Z that identifies P(target | do(source))
    /// from observational data alone, or surfaces the open back-door
    /// paths that prevent identification.
    ///
    /// The link graph used: `depends` and `supports` edges. Every
    /// finding's parents are the findings it relies on as evidence;
    /// every finding's children are the findings that build on it.
    /// `contradicts` and other link types are excluded from the
    /// causal DAG.
    Effect {
        frontier: PathBuf,
        /// Source finding id (`vf_<hash>`).
        source: String,
        /// Target finding id, given via `--on`.
        #[arg(long)]
        on: String,
        #[arg(long)]
        json: bool,
    },
    /// v0.44: Print the causal-graph topology over the frontier.
    /// Lists each node's parents and children for inspection.
    Graph {
        frontier: PathBuf,
        /// Limit output to a single node's neighborhood.
        #[arg(long)]
        node: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// v0.45 (Pearl level 3): answer a counterfactual query of the form
    /// "if we had observed `intervene_on` at `value`, what would
    /// `target`'s confidence have been?" Twin-network propagation
    /// requires every edge on the source→target paths to declare a
    /// `mechanism`; edges without one block propagation honestly with
    /// a `mechanism_unspecified` verdict.
    Counterfactual {
        frontier: PathBuf,
        /// The finding to intervene on (`vf_<hash>`).
        intervene_on: String,
        /// The confidence value to set on the intervened finding (in [0,1]).
        #[arg(long)]
        set_to: f64,
        /// The target finding whose counterfactual confidence we want (`vf_<hash>`).
        #[arg(long)]
        target: String,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum BridgesAction {
    /// Derive bridges between two frontiers and persist the resulting
    /// `vbr_<id>` records under the *first* frontier's `.vela/bridges/`
    /// directory. Idempotent on (entity, sorted-frontier-pair).
    Derive {
        /// First frontier (Vela repo or frontier JSON file).
        /// Bridges are persisted under this frontier.
        frontier_a: PathBuf,
        /// Human label for the first frontier in bridge records.
        #[arg(long, default_value = "a")]
        label_a: String,
        /// Second frontier (Vela repo or frontier JSON file).
        frontier_b: PathBuf,
        /// Human label for the second frontier in bridge records.
        #[arg(long, default_value = "b")]
        label_b: String,
        #[arg(long)]
        json: bool,
    },
    /// List bridges persisted under a frontier's `.vela/bridges/` dir.
    List {
        /// Frontier (must be a Vela repo with a `.vela/` directory).
        frontier: PathBuf,
        /// Filter by status: derived, confirmed, refuted.
        #[arg(long)]
        status: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// Show a single bridge by `vbr_<id>`.
    Show {
        frontier: PathBuf,
        bridge_id: String,
        #[arg(long)]
        json: bool,
    },
    /// Promote a bridge from `derived` to `confirmed`. Persists in
    /// place; the content-address `vbr_<id>` is unchanged. v0.67:
    /// emits a `bridge.reviewed` canonical event under the configured
    /// reviewer id so federation sync can propagate the verdict.
    Confirm {
        frontier: PathBuf,
        bridge_id: String,
        /// Reviewer identity attaching the verdict. Defaults to
        /// $VELA_REVIEWER_ID or `reviewer:will-blair`.
        #[arg(long)]
        reviewer: Option<String>,
        /// Optional verdict note.
        #[arg(long)]
        note: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// Mark a bridge `refuted`. Persists in place. v0.67: emits a
    /// `bridge.reviewed` canonical event with `status: refuted`.
    Refute {
        frontier: PathBuf,
        bridge_id: String,
        #[arg(long)]
        reviewer: Option<String>,
        #[arg(long)]
        note: Option<String>,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum FederationAction {
    /// v0.39: Register a peer hub in this frontier. Adding a peer
    /// declares awareness — it does not trust their state. Sync /
    /// merge runtime ships in v0.39.1+.
    PeerAdd {
        frontier: PathBuf,
        /// Stable peer id (e.g. `hub:vela-mirror-eu`).
        id: String,
        /// HTTPS URL where the peer publishes signed manifests.
        #[arg(long)]
        url: String,
        /// Hex-encoded Ed25519 public key (64 hex chars).
        #[arg(long)]
        pubkey: String,
        /// Optional human-readable note (e.g. "EU mirror, run by lab Z").
        #[arg(long, default_value = "")]
        note: String,
        #[arg(long)]
        json: bool,
    },
    /// List federation peers registered in a frontier.
    PeerList {
        frontier: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Remove a peer from the registry. Does not retroactively
    /// invalidate events that referenced the peer; just stops further
    /// sync attempts.
    PeerRemove {
        frontier: PathBuf,
        id: String,
        #[arg(long)]
        json: bool,
    },
    /// v0.39.1 / v0.41.0: Sync our frontier against a peer's
    /// published view. Three modes:
    ///   1. `--via-hub --vfr-id <id>`: route through the peer hub's
    ///      `/entries/<vfr_id>` endpoint, verify the registry entry
    ///      signature, follow the locator. The "real federation"
    ///      path. Surfaces broken-locator and unverified-entry
    ///      conflicts when the peer is reachable but stale.
    ///   2. `--url <override>`: fetch directly from a manifest URL,
    ///      bypassing the hub's registry. Useful for static-mirror
    ///      peers (raw GitHub) or for testing.
    ///   3. (default): tries `<peer.url>/manifest/<frontier_id>.json`.
    /// Diffs the resulting Project against ours, appends one
    /// `frontier.synced_with_peer` event + one
    /// `frontier.conflict_detected` event per disagreement.
    /// Read-only with respect to findings; conflict resolution
    /// happens through subsequent reviewer-signed proposals.
    Sync {
        frontier: PathBuf,
        /// Peer id (must already be in the registry).
        peer_id: String,
        /// Direct manifest URL override.
        #[arg(long)]
        url: Option<String>,
        /// Route through the peer hub's `/entries/<vfr-id>` endpoint
        /// (verify entry signature, follow locator). Requires
        /// `--vfr-id`.
        #[arg(long)]
        via_hub: bool,
        /// vfr_id to fetch when using `--via-hub`. Defaults to our
        /// local frontier_id when omitted.
        #[arg(long)]
        vfr_id: Option<String>,
        /// v0.64: opt-in flag to allow `--via-hub --vfr-id <peer_vfr>`
        /// where `<peer_vfr>` differs from the local frontier's id.
        /// Without this flag, cross-vfr sync is refused because every
        /// peer-side finding gets recorded as a "missing_locally"
        /// conflict, flooding the inbox with substrate-honest but
        /// operationally noisy events.
        #[arg(long)]
        allow_cross_vfr: bool,
        /// Run the diff but don't append events.
        #[arg(long)]
        dry_run: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.70: Push a single locally-resolved
    /// `frontier.conflict_resolved` event back to the originating
    /// peer hub. Reads the event from the local frontier, signs the
    /// canonical bytes with the supplied private key (or the actor's
    /// key under `~/.config/vela/keys/`), and POSTs to the peer's
    /// `/entries/<vfr_id>/events` endpoint with paired
    /// `X-Vela-Signer-Pubkey` and `X-Vela-Signature` headers.
    /// One event at a time; the hub validates signature, actor
    /// pubkey, pairing against an existing
    /// `frontier.conflict_detected`, and idempotency on the
    /// resolution. Subsequent `vela federation sync` calls against
    /// that hub return the resolution to anyone else who pulls.
    PushResolution {
        frontier: PathBuf,
        /// The id of the original `frontier.conflict_detected`
        /// event whose paired `frontier.conflict_resolved` event
        /// should be pushed.
        conflict_event_id: String,
        /// Peer id (must already be in the registry).
        #[arg(long = "to")]
        to: String,
        /// Path to the actor's Ed25519 private key file (hex). If
        /// omitted, looks up `~/.config/vela/keys/<actor_id>.key`,
        /// then `~/.config/vela/keys/private.key`.
        #[arg(long)]
        key: Option<PathBuf>,
        /// Override the vfr_id sent to the peer (defaults to the
        /// local frontier_id).
        #[arg(long)]
        vfr_id: Option<String>,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum FrontierAction {
    /// Scaffold a fresh, publishable `frontier.json` stub. The result
    /// passes `vela check --strict` immediately and is ready to accept
    /// findings via `vela finding add` and a publish via `vela registry
    /// publish`. Use this instead of `vela init` when you intend to
    /// publish to a hub — `init` creates a `.vela/` repo, which is not
    /// directly publishable in v0.
    New {
        /// Path to write the new frontier file (e.g. `./frontier.json`).
        path: PathBuf,
        /// Human-readable frontier name.
        #[arg(long)]
        name: String,
        /// Optional one-paragraph description of the bounded question.
        #[arg(long, default_value = "")]
        description: String,
        /// Overwrite if the file already exists.
        #[arg(long)]
        force: bool,
        #[arg(long)]
        json: bool,
    },
    /// Replay a split frontier repository into frontier.json and vela.lock.
    Materialize {
        /// Frontier repository directory.
        frontier: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Declare a cross-frontier dependency. Subsequent links of the
    /// form `vf_<id>@vfr_<id>` resolve through this entry; strict
    /// validation refuses cross-frontier targets without one.
    AddDep {
        /// Path to the frontier file
        frontier: PathBuf,
        /// The remote frontier's content-addressed id (`vfr_…`)
        vfr_id: String,
        /// Where to fetch the remote frontier file from. Typically
        /// an `https://…` URL pointing at raw JSON.
        #[arg(long)]
        locator: String,
        /// SHA-256 of the remote's canonical snapshot. Strict pull
        /// verifies the fetched dependency's snapshot matches this.
        #[arg(long)]
        snapshot: String,
        /// Optional human-readable name for the dependency.
        #[arg(long)]
        name: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// List the frontier's declared dependencies.
    ListDeps {
        frontier: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Remove a previously-declared cross-frontier dependency by `vfr_id`.
    /// Refuses if any link target still references it.
    RemoveDep {
        frontier: PathBuf,
        vfr_id: String,
        #[arg(long)]
        json: bool,
    },
    /// v0.11: re-pin every declared cross-frontier dependency to the
    /// hub's current snapshot for that `vfr_id`. Useful when a dep
    /// (e.g. BBB) republishes weekly and your local pin goes stale.
    /// Reports per-dep status: unchanged, refreshed (with old → new
    /// snapshot), missing (vfr_id not on hub), or unreachable. Does
    /// nothing destructive if --dry-run is passed.
    RefreshDeps {
        frontier: PathBuf,
        /// Hub URL to query. Defaults to https://vela-hub.fly.dev.
        #[arg(long, default_value = "https://vela-hub.fly.dev")]
        from: String,
        /// Show what would change without writing.
        #[arg(long)]
        dry_run: bool,
        #[arg(long)]
        json: bool,
    },
    /// v0.32: emit a structured diff of findings added, updated, and
    /// contradicted in a time window. The canonical replacement for the
    /// `scripts/weekly-diff.sh` Python fallback shipped in v0.31.
    ///
    /// Default window is the current ISO week (Monday 00:00 UTC →
    /// next Monday 00:00 UTC). Use `--since <RFC3339>` for an arbitrary
    /// start, or `--week YYYY-Www` for a specific ISO week.
    ///
    /// Output is JSON if `--json` is set; otherwise a human summary.
    /// The diff is read-only over the canonical state — it does not
    /// modify the frontier and does not require a signing key.
    Diff {
        /// Path to the frontier (project dir, `.vela/` repo, or `.json` file).
        frontier: PathBuf,
        /// Compute diff since this RFC 3339 timestamp.
        /// Mutually exclusive with `--week`.
        #[arg(long)]
        since: Option<String>,
        /// Compute diff for a specific ISO week (e.g. `2026-W18`).
        /// If absent and no `--since`, defaults to the current ISO week.
        #[arg(long)]
        week: Option<String>,
        /// Emit JSON to stdout.
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum RepoAction {
    /// Show materialization, proof, proposal, and hash status.
    Status {
        /// Frontier repository directory.
        frontier: PathBuf,
        /// Output stable JSON.
        #[arg(long)]
        json: bool,
    },
    /// Check folder shape, manifest paths, stale proof, and root clutter.
    Doctor {
        /// Frontier repository directory.
        frontier: PathBuf,
        /// Output stable JSON.
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum QueueAction {
    /// List queued draft actions (no signing)
    List {
        #[arg(long)]
        queue_file: Option<PathBuf>,
        #[arg(long)]
        json: bool,
    },
    /// Sign each queued draft with the actor's Ed25519 key and apply
    /// it locally. Removes signed entries from the queue on success.
    Sign {
        /// Stable actor id matching a registered entry in the frontier
        #[arg(long)]
        actor: String,
        /// Path to the actor's Ed25519 private key (hex-encoded)
        #[arg(long)]
        key: PathBuf,
        /// Override the queue file location
        #[arg(long)]
        queue_file: Option<PathBuf>,
        /// Skip per-action confirmation prompts and sign every queued
        /// draft. Required in non-interactive contexts. The `--all`
        /// alias is accepted for muscle-memory convenience (the v0.28
        /// sim-user docs and an early friction report both wrote it
        /// that way; cheaper to accept the alias than to retrain).
        #[arg(long, alias = "all")]
        yes_to_all: bool,
        #[arg(long)]
        json: bool,
    },
    /// Drop all queued draft actions
    Clear {
        #[arg(long)]
        queue_file: Option<PathBuf>,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum RegistryAction {
    /// List all entries in a local registry
    List {
        /// Path or file:// URL of the registry; defaults to ~/.vela/registry/entries.json
        #[arg(long)]
        from: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// Publish a frontier's current snapshot+event_log hashes to a registry
    Publish {
        /// Path to the frontier file
        frontier: PathBuf,
        /// Stable owner actor id (must be registered in the frontier)
        #[arg(long)]
        owner: String,
        /// Path to the owner's Ed25519 private key (hex-encoded)
        #[arg(long)]
        key: PathBuf,
        /// Network locator under which the frontier is reachable
        /// (file:// path or HTTP URL the publisher serves). Optional
        /// since v0.55: when publishing to an HTTP hub, the hub's own
        /// `/entries/<vfr>/snapshot` URL is auto-filled if omitted, and
        /// the substrate is uploaded inline so locator divergence is
        /// no longer a failure mode.
        #[arg(long)]
        locator: Option<String>,
        /// Registry to publish to (path/URL); default ~/.vela/registry/entries.json
        #[arg(long)]
        to: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// v0.15: list registry entries whose frontier declares a
    /// cross-frontier dependency on the given `vfr_id`. Surfaces
    /// "who is referencing my frontier" — the bidirectional view
    /// of cross-frontier composition. Hub-only (no local-registry
    /// equivalent yet); requires the hub to support
    /// `GET /entries/{vfr_id}/depends-on`.
    DependsOn {
        /// Frontier address (`vfr_…`) to look up dependents of.
        vfr_id: String,
        /// Hub URL. Required for v0.15 (no local file walk yet).
        #[arg(long, default_value = "https://vela-hub.fly.dev")]
        from: String,
        #[arg(long)]
        json: bool,
    },
    /// v0.20: federation primitive. Pull a signed manifest from one hub
    /// (`--from`) and POST it verbatim to another (`--to`). Both hubs
    /// validate the signature against the manifest's embedded
    /// `owner_pubkey`; mirroring is a no-op for authenticity. Use this
    /// to replicate a frontier across hubs (resilience), seed a fresh
    /// hub from an established one, or test a hub deployment with real
    /// signed bytes.
    Mirror {
        /// Frontier address (`vfr_…`) to mirror.
        vfr_id: String,
        /// Source hub URL.
        #[arg(long)]
        from: String,
        /// Destination hub URL.
        #[arg(long)]
        to: String,
        #[arg(long)]
        json: bool,
    },
    /// Pull and verify a frontier from a registry by `vfr_id`
    Pull {
        /// Frontier address (`vfr_…`)
        vfr_id: String,
        /// Registry to pull from
        #[arg(long)]
        from: Option<String>,
        /// Output path for the pulled frontier. With --transitive, this
        /// is the directory dependencies are also written into; without
        /// it, this is the file path the primary lands at.
        #[arg(long)]
        out: PathBuf,
        /// v0.8: also pull every cross-frontier dependency the primary
        /// declares, recursively, verifying each pinned snapshot.
        #[arg(long)]
        transitive: bool,
        /// v0.8: maximum recursion depth when --transitive is set.
        /// Primary is depth 0; its direct deps are depth 1.
        #[arg(long, default_value = "4")]
        depth: usize,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum GapsAction {
    /// Rank candidate gap review leads
    Rank {
        frontier: PathBuf,
        #[arg(long, default_value = "10")]
        top: usize,
        #[arg(long)]
        domain: Option<String>,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum LinkAction {
    /// Append a typed link from one finding to another. The target
    /// may be a local `vf_<hex>` or a cross-frontier `vf_<hex>@vfr_<hex>`
    /// (v0.8). Cross-frontier targets require a matching declared dep —
    /// run `vela frontier add-dep` first or strict validation will refuse.
    Add {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Source finding id (`vf_<hex>`)
        #[arg(long)]
        from: String,
        /// Target. Either `vf_<hex>` (local) or `vf_<hex>@vfr_<hex>` (cross).
        #[arg(long)]
        to: String,
        /// Link type. One of: supports, contradicts, extends, depends, replicates, supersedes, synthesized_from
        #[arg(long, default_value = "supports")]
        r#type: String,
        /// Optional human-readable note
        #[arg(long, default_value = "")]
        note: String,
        /// Who inferred the link. One of: compiler, reviewer, author
        #[arg(long, default_value = "reviewer")]
        inferred_by: String,
        /// v0.16: skip the cross-frontier target-status check. By
        /// default, when adding a cross-frontier link, the substrate
        /// fetches the dep's frontier from its declared locator and
        /// warns if the target finding has `flags.superseded = true`
        /// (you'd be linking to an outdated wording). The link is
        /// still recorded — this is a best-effort review hint, not a
        /// hard refusal. Set this flag to skip the network fetch
        /// (useful in CI or when offline).
        #[arg(long)]
        no_check_target: bool,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum EntityAction {
    /// Walk every finding's entities and try to resolve each against
    /// the bundled common-entity table. Matched entities get
    /// `canonical_id` populated, `resolution_method = manual`,
    /// `resolution_confidence = 0.95`, `needs_review = false`. Already-
    /// resolved entities are skipped unless `--force` is passed. The
    /// frontier file is written back atomically.
    Resolve {
        frontier: PathBuf,
        /// Re-resolve entities that already have a canonical_id.
        #[arg(long)]
        force: bool,
        #[arg(long)]
        json: bool,
    },
    /// List the bundled lookup table.
    List {
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum FindingCommands {
    /// Add a manual finding bundle with an assertion field
    Add {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Assertion text inside the finding bundle
        #[arg(long)]
        assertion: String,
        /// Assertion type. One of: mechanism, therapeutic, diagnostic, epidemiological, observational, review, methodological, computational, theoretical, negative
        #[arg(long, default_value = "mechanism")]
        r#type: String,
        /// Source label for the finding
        #[arg(long, default_value = "manual finding")]
        source: String,
        /// Source type. One of: published_paper, preprint, clinical_trial, lab_notebook, model_output, expert_assertion, database_record
        #[arg(long, default_value = "expert_assertion")]
        source_type: String,
        /// Author/reviewer identifier
        #[arg(long)]
        author: String,
        /// Initial confidence score from 0.0 to 1.0
        #[arg(long, default_value = "0.3")]
        confidence: f64,
        /// Evidence type. One of: experimental, observational, computational, theoretical, meta_analysis, systematic_review, case_report
        #[arg(long, default_value = "theoretical")]
        evidence_type: String,
        /// Entities as comma-separated name:type pairs. Entity types: gene, protein, compound, disease, cell_type, organism, pathway, assay, anatomical_structure, particle, instrument, dataset, quantity, other
        #[arg(long, default_value = "")]
        entities: String,
        /// Mark manually supplied entities as curator-reviewed
        #[arg(long)]
        entities_reviewed: bool,
        /// Evidence span text or JSON. Repeat to attach multiple source spans
        #[arg(long)]
        evidence_span: Vec<String>,
        /// Mark this finding as a candidate gap
        #[arg(long)]
        gap: bool,
        /// Mark this finding as negative-space evidence
        #[arg(long)]
        negative_space: bool,
        /// v0.11: DOI of the source artifact (e.g. "10.1038/s41586-024-...")
        #[arg(long)]
        doi: Option<String>,
        /// v0.11: PubMed ID
        #[arg(long)]
        pmid: Option<String>,
        /// v0.11: Publication year
        #[arg(long)]
        year: Option<i32>,
        /// v0.11: Journal name
        #[arg(long)]
        journal: Option<String>,
        /// v0.11: Generic source URL when none of the structured identifiers fit
        #[arg(long)]
        url: Option<String>,
        /// v0.11: Source-paper authors as semicolon-separated list (distinct from --author which is the curating Vela actor)
        #[arg(long)]
        source_authors: Option<String>,
        /// v0.11: Conditions/scope text. Replaces the placeholder otherwise written. Should describe scope boundaries (species, dosing, age range, model, etc.)
        #[arg(long)]
        conditions_text: Option<String>,
        /// v0.11: Verified species as semicolon-separated list (e.g. "Mus musculus;Homo sapiens")
        #[arg(long)]
        species: Option<String>,
        /// v0.11: Mark the finding as in vivo
        #[arg(long)]
        in_vivo: bool,
        /// v0.11: Mark the finding as in vitro
        #[arg(long)]
        in_vitro: bool,
        /// v0.11: Mark the finding as having human data
        #[arg(long)]
        human_data: bool,
        /// v0.11: Mark the finding as a clinical trial
        #[arg(long)]
        clinical_trial: bool,
        /// Output stable JSON
        #[arg(long)]
        json: bool,
        /// Immediately accept and apply the proposal locally
        #[arg(long)]
        apply: bool,
    },
    /// v0.14: Supersede an existing finding with a new content-addressed
    /// claim. The new finding gets its own `vf_…` id; an auto-injected
    /// `supersedes` link points back at the old id; the old finding is
    /// flagged `superseded`. Both remain queryable. Real corrections
    /// (Phase 4 follow-up data, retraction, refined wording) belong here
    /// rather than as caveats stacked on top of an immutable claim.
    Supersede {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// `vf_…` id of the finding to supersede
        old_id: String,
        /// New assertion text (drives the new finding's content address)
        #[arg(long)]
        assertion: String,
        /// New assertion type
        #[arg(long, default_value = "mechanism")]
        r#type: String,
        /// Source label
        #[arg(long, default_value = "manual finding")]
        source: String,
        /// Source type
        #[arg(long, default_value = "expert_assertion")]
        source_type: String,
        /// Curating Vela actor id
        #[arg(long)]
        author: String,
        /// Reason for the supersede (becomes the proposal/event reason)
        #[arg(long)]
        reason: String,
        /// New confidence score 0.0..=1.0
        #[arg(long, default_value = "0.5")]
        confidence: f64,
        /// New evidence type
        #[arg(long, default_value = "experimental")]
        evidence_type: String,
        /// New entities (`name:type` pairs, comma-separated)
        #[arg(long, default_value = "")]
        entities: String,
        /// DOI of the source artifact
        #[arg(long)]
        doi: Option<String>,
        /// PubMed ID
        #[arg(long)]
        pmid: Option<String>,
        /// Publication year
        #[arg(long)]
        year: Option<i32>,
        /// Journal name
        #[arg(long)]
        journal: Option<String>,
        /// Generic source URL
        #[arg(long)]
        url: Option<String>,
        /// Source-paper authors (semicolon-separated)
        #[arg(long)]
        source_authors: Option<String>,
        /// Conditions/scope text
        #[arg(long)]
        conditions_text: Option<String>,
        /// Verified species (semicolon-separated)
        #[arg(long)]
        species: Option<String>,
        #[arg(long)]
        in_vivo: bool,
        #[arg(long)]
        in_vitro: bool,
        #[arg(long)]
        human_data: bool,
        #[arg(long)]
        clinical_trial: bool,
        #[arg(long)]
        json: bool,
        /// Immediately accept and apply the proposal locally
        #[arg(long)]
        apply: bool,
    },
    /// v0.38: Set or revise the Pearlian causal type and study-design
    /// grade for a finding. Appends an `assertion.reinterpreted_causal`
    /// event capturing the prior reading, the new reading, and the
    /// reviewer who re-graded. Pre-v0.38 findings carry no causal
    /// metadata; the first call materializes both fields.
    CausalSet {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// `vf_<id>` of the finding to re-grade.
        finding_id: String,
        /// Causal claim kind: correlation | mediation | intervention.
        #[arg(long)]
        claim: String,
        /// Optional study-design grade: rct | quasi_experimental |
        /// observational | theoretical.
        #[arg(long)]
        grade: Option<String>,
        /// Reviewer/curator id (must match a registered actor under
        /// `--strict`). Recorded on the appended event.
        #[arg(long)]
        actor: String,
        /// One-paragraph reason. Becomes the event's `reason` field
        /// and ships with the proposal.
        #[arg(long)]
        reason: String,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum ProposalAction {
    /// List proposals in a frontier
    List {
        frontier: PathBuf,
        #[arg(long)]
        status: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// Show one proposal
    Show {
        frontier: PathBuf,
        proposal_id: String,
        #[arg(long)]
        json: bool,
    },
    /// Preview applying one proposal without mutating the frontier
    Preview {
        frontier: PathBuf,
        proposal_id: String,
        #[arg(long, default_value = "reviewer:preview")]
        reviewer: String,
        #[arg(long)]
        json: bool,
    },
    /// Import proposal files into a frontier
    Import {
        frontier: PathBuf,
        source: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Validate standalone proposal files or directories
    Validate {
        source: PathBuf,
        #[arg(long)]
        json: bool,
    },
    /// Export proposal records from a frontier
    Export {
        frontier: PathBuf,
        output: PathBuf,
        #[arg(long)]
        status: Option<String>,
        #[arg(long)]
        json: bool,
    },
    /// Accept and apply one proposal
    Accept {
        frontier: PathBuf,
        proposal_id: String,
        #[arg(long)]
        reviewer: String,
        #[arg(long)]
        reason: String,
        #[arg(long)]
        json: bool,
    },
    /// Reject one proposal
    Reject {
        frontier: PathBuf,
        proposal_id: String,
        #[arg(long)]
        reviewer: String,
        #[arg(long)]
        reason: String,
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum SourceAdapterAction {
    /// Run a source adapter over a frontier-owned ingest plan
    Run {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Adapter id. Currently: clinicaltrials-gov-v2 or regulatory-documents-v1
        adapter: String,
        /// Stable actor id recorded on generated proposals
        #[arg(long)]
        actor: String,
        /// Restrict to source ingest entry ids
        #[arg(long = "entry")]
        entries: Vec<String>,
        /// Restrict to P0, P1, or P2 entries
        #[arg(long)]
        priority: Option<String>,
        /// Include entries marked excluded
        #[arg(long)]
        include_excluded: bool,
        /// Continue when one source record fails
        #[arg(long)]
        allow_partial: bool,
        /// Report planned work without writing packets, proposals, or run files
        #[arg(long)]
        dry_run: bool,
        /// Read saved source fixtures from this directory
        #[arg(long)]
        input_dir: Option<PathBuf>,
        /// Apply artifact proposals while leaving truth changes pending
        #[arg(long)]
        apply_artifacts: bool,
        /// Emit JSON to stdout
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum RuntimeAdapterAction {
    /// Normalize an external runtime export into reviewable frontier proposals
    Run {
        /// Frontier JSON file or Vela repo
        frontier: PathBuf,
        /// Adapter id. Currently: scienceclaw-artifact-v1 or agent-discourse-v1
        adapter: String,
        /// External runtime export JSON file or directory
        #[arg(long)]
        input: PathBuf,
        /// Stable actor id recorded on generated proposals
        #[arg(long)]
        actor: String,
        /// Report planned work without writing packets, proposals, or run files
        #[arg(long)]
        dry_run: bool,
        /// Apply artifact proposals while leaving truth changes pending
        #[arg(long)]
        apply_artifacts: bool,
        /// Emit JSON to stdout
        #[arg(long)]
        json: bool,
    },
}

#[derive(Subcommand)]
enum BridgeKitAction {
    /// Validate one packet JSON file or a directory of packet JSON files
    Validate {
        /// Packet JSON file or directory
        source: PathBuf,
        /// Emit JSON to stdout
        #[arg(long)]
        json: bool,
    },
    /// v0.108.3: Verify that DOIs and PMIDs claimed in a Carina
    /// packet's artifact locators and candidate-claim source_refs
    /// actually resolve through Crossref / PubMed eutils. Closes
    /// part of THREAT_MODEL.md A6 (citation poisoning: a fabricated
    /// DOI passes structural validation today). Network call;
    /// skips identifiers if the upstream is unreachable.
    VerifyProvenance {
        /// Packet JSON file
        packet: PathBuf,
        /// Emit JSON to stdout
        #[arg(long)]
        json: bool,
    },
}

pub async fn run_command() {
    dotenvy::dotenv().ok();

    match Cli::parse().command {
        Commands::Scout {
            folder,
            frontier,
            backend,
            dry_run,
            json,
        } => {
            cmd_scout(&folder, &frontier, backend.as_deref(), dry_run, json).await;
        }
        Commands::CompileNotes {
            vault,
            frontier,
            backend,
            max_files,
            max_items_per_category,
            dry_run,
            json,
        } => {
            cmd_compile_notes(
                &vault,
                &frontier,
                backend.as_deref(),
                max_files,
                max_items_per_category,
                dry_run,
                json,
            )
            .await;
        }
        Commands::CompileCode {
            root,
            frontier,
            backend,
            max_files,
            dry_run,
            json,
        } => {
            cmd_compile_code(
                &root,
                &frontier,
                backend.as_deref(),
                max_files,
                dry_run,
                json,
            )
            .await;
        }
        Commands::CompileData {
            root,
            frontier,
            backend,
            sample_rows,
            dry_run,
            json,
        } => {
            cmd_compile_data(
                &root,
                &frontier,
                backend.as_deref(),
                sample_rows,
                dry_run,
                json,
            )
            .await;
        }
        Commands::ReviewPending {
            frontier,
            backend,
            max_proposals,
            batch_size,
            dry_run,
            json,
        } => {
            cmd_review_pending(
                &frontier,
                backend.as_deref(),
                max_proposals,
                batch_size,
                dry_run,
                json,
            )
            .await;
        }
        Commands::FindTensions {
            frontier,
            backend,
            max_findings,
            dry_run,
            json,
        } => {
            cmd_find_tensions(&frontier, backend.as_deref(), max_findings, dry_run, json).await;
        }
        Commands::PlanExperiments {
            frontier,
            backend,
            max_findings,
            dry_run,
            json,
        } => {
            cmd_plan_experiments(&frontier, backend.as_deref(), max_findings, dry_run, json).await;
        }
        Commands::Check {
            source,
            schema,
            stats,
            conformance,
            conformance_dir,
            all,
            schema_only,
            strict,
            fix,
            json,
        } => cmd_check(
            source.as_deref(),
            schema,
            stats,
            conformance,
            &conformance_dir,
            all,
            schema_only,
            strict,
            fix,
            json,
        ),
        Commands::Integrity { frontier, json } => cmd_integrity(&frontier, json),
        Commands::Impact {
            frontier,
            finding_id,
            depth,
            json,
        } => cmd_impact(&frontier, &finding_id, depth, json),
        Commands::Discord {
            frontier,
            json,
            kind,
        } => cmd_discord(&frontier, json, kind.as_deref()),
        Commands::Normalize {
            source,
            out,
            write,
            dry_run,
            rewrite_ids,
            id_map,
            resync_provenance,
            json,
        } => cmd_normalize(
            &source,
            out.as_deref(),
            write,
            dry_run,
            rewrite_ids,
            id_map.as_deref(),
            resync_provenance,
            json,
        ),
        Commands::Proof {
            frontier,
            out,
            template,
            gold,
            record_proof_state,
            json,
        } => cmd_proof(
            &frontier,
            &out,
            &template,
            gold.as_deref(),
            record_proof_state,
            json,
        ),
        Commands::Repo { action } => cmd_repo(action),
        Commands::Serve {
            frontier,
            frontiers,
            backend,
            http,
            setup,
            check_tools,
            json,
            workbench,
        } => {
            if setup {
                cmd_mcp_setup(frontier.as_deref(), frontiers.as_deref());
            } else if check_tools {
                let source =
                    serve::ProjectSource::from_args(frontier.as_deref(), frontiers.as_deref());
                match serve::check_tools(source) {
                    Ok(report) => {
                        if json {
                            println!(
                                "{}",
                                serde_json::to_string_pretty(&report)
                                    .expect("failed to serialize tool check report")
                            );
                        } else {
                            print_tool_check_report(&report);
                        }
                    }
                    Err(e) => fail(&format!("Tool check failed: {e}")),
                }
            } else {
                let source =
                    serve::ProjectSource::from_args(frontier.as_deref(), frontiers.as_deref());
                // Phase R: --workbench implies HTTP and serves web/.
                let resolved_port = if workbench {
                    Some(http.unwrap_or(3848))
                } else {
                    http
                };
                if let Some(port) = resolved_port {
                    serve::run_http(source, backend.as_deref(), port, workbench).await;
                } else {
                    serve::run(source, backend.as_deref()).await;
                }
            }
        }
        Commands::Status { frontier, json } => cmd_status(&frontier, json),
        Commands::Log {
            frontier,
            limit,
            kind,
            json,
        } => cmd_log(&frontier, limit, kind.as_deref(), json),
        Commands::Inbox {
            frontier,
            kind,
            limit,
            json,
        } => cmd_inbox(&frontier, kind.as_deref(), limit, json),
        Commands::Ask {
            frontier,
            question,
            json,
        } => cmd_ask(&frontier, &question.join(" "), json),
        Commands::Stats { frontier, json } => {
            if json {
                print_stats_json(&frontier);
            } else {
                cmd_stats(&frontier);
            }
        }
        Commands::Search {
            source,
            query,
            entity,
            r#type,
            all,
            limit,
            json,
        } => cmd_search(
            source.as_deref(),
            &query,
            entity.as_deref(),
            r#type.as_deref(),
            all.as_deref(),
            limit,
            json,
        ),
        Commands::Tensions {
            source,
            both_high,
            cross_domain,
            top,
            json,
        } => cmd_tensions(&source, both_high, cross_domain, top, json),
        Commands::Gaps { action } => cmd_gaps(action),
        Commands::Bridge {
            inputs,
            novelty,
            top,
        } => cmd_bridge(&inputs, novelty, top).await,
        Commands::Export {
            frontier,
            format,
            output,
        } => export::run(&frontier, &format, output.as_deref()),
        Commands::Packet { action } => cmd_packet(action),
        Commands::Verify { path, json } => cmd_verify(&path, json),
        Commands::Bench {
            frontier,
            gold,
            candidate,
            sources,
            threshold,
            report,
            entity_gold,
            link_gold,
            suite,
            suite_ready,
            min_f1,
            min_precision,
            min_recall,
            no_thresholds,
            json,
        } => {
            // v0.26 VelaBench routing: presence of `--candidate`
            // selects the agent state-update scorer. The legacy
            // extraction harness keeps every other invocation
            // unchanged.
            if let Some(cand) = candidate.clone() {
                let Some(g) = gold.clone() else {
                    eprintln!(
                        "{} `vela bench --candidate <…>` requires `--gold <…>`",
                        style::err_prefix()
                    );
                    std::process::exit(2);
                };
                cmd_agent_bench(
                    &g,
                    &cand,
                    sources.as_deref(),
                    threshold,
                    report.as_deref(),
                    json,
                );
            } else {
                cmd_bench(BenchArgs {
                    frontier,
                    gold,
                    entity_gold,
                    link_gold,
                    suite,
                    suite_ready,
                    min_f1,
                    min_precision,
                    min_recall,
                    no_thresholds,
                    json,
                });
            }
        }
        Commands::Conformance { dir } => {
            let _ = conformance::run(&dir);
        }
        Commands::Version => println!("vela 0.36.0"),
        Commands::Sign { action } => cmd_sign(action),
        Commands::Actor { action } => cmd_actor(action),
        Commands::Federation { action } => cmd_federation(action),
        Commands::Causal { action } => cmd_causal(action),
        Commands::Frontier { action } => cmd_frontier(action),
        Commands::Queue { action } => cmd_queue(action),
        Commands::Registry { action } => cmd_registry(action),
        Commands::Init {
            path,
            name,
            template,
            no_git,
            json,
        } => cmd_init(&path, &name, &template, !no_git, json),
        Commands::Quickstart {
            path,
            name,
            reviewer,
            assertion,
            keys_out,
            json,
        } => cmd_quickstart(
            &path,
            &name,
            &reviewer,
            assertion.as_deref(),
            keys_out.as_deref(),
            json,
        ),
        Commands::Lock { path, check, json } => cmd_lock(&path, check, json),
        Commands::Doc { path, out, json } => cmd_doc(&path, out.as_deref(), json),
        Commands::Import { frontier, into } => cmd_import(&frontier, into.as_deref()),
        Commands::Diff {
            target,
            frontier_b,
            frontier,
            reviewer,
            json,
            quiet,
        } => {
            // v0.74.3: if the first positional looks like a
            // proposal id, route to proposals preview. Otherwise
            // treat it as a frontier path and run the two-frontier
            // diff.
            if target.starts_with("vpr_") {
                let frontier_root = frontier
                    .clone()
                    .or_else(|| frontier_b.clone())
                    .unwrap_or_else(|| std::path::PathBuf::from("."));
                let preview = proposals::preview_at_path(&frontier_root, &target, &reviewer)
                    .unwrap_or_else(|e| fail_return(&e));
                let payload = json!({
                    "ok": true,
                    "command": "diff.proposal",
                    "frontier": frontier_root.display().to_string(),
                    "proposal_id": target,
                    "preview": preview,
                });
                if json {
                    println!(
                        "{}",
                        serde_json::to_string_pretty(&payload)
                            .expect("failed to serialize diff preview")
                    );
                } else {
                    println!("vela diff · proposal preview");
                    println!("  proposal: {}", target);
                    println!("  kind: {}", preview.kind);
                    println!(
                        "  findings: {} -> {}",
                        preview.findings_before, preview.findings_after
                    );
                    println!(
                        "  artifacts: {} -> {}",
                        preview.artifacts_before, preview.artifacts_after
                    );
                    println!(
                        "  events: {} -> {}",
                        preview.events_before, preview.events_after
                    );
                    if !preview.changed_findings.is_empty() {
                        println!(
                            "  findings changed: {}",
                            preview.changed_findings.join(", ")
                        );
                    }
                }
            } else {
                let frontier_a = std::path::PathBuf::from(&target);
                let b = frontier_b.unwrap_or_else(|| {
                    fail_return(
                        "diff: two-frontier mode needs a second positional path; for proposal preview pass a `vpr_*` id",
                    )
                });
                diff::run(&frontier_a, &b, json, quiet);
            }
        }
        Commands::Proposals { action } => cmd_proposals(action),
        Commands::ArtifactToState {
            frontier,
            packet,
            actor,
            apply_artifacts,
            json,
        } => cmd_artifact_to_state(&frontier, &packet, &actor, apply_artifacts, json),
        Commands::BridgeKit { action } => cmd_bridge_kit(action).await,
        Commands::SourceAdapter { action } => cmd_source_adapter(action).await,
        Commands::RuntimeAdapter { action } => cmd_runtime_adapter(action),
        Commands::Link { action } => cmd_link(action),
        Commands::Workbench {
            path,
            port,
            no_open,
        } => {
            if let Err(e) = crate::workbench::run(path, port, !no_open).await {
                fail(&e);
            }
        }
        Commands::Bridges { action } => cmd_bridges(action),
        Commands::Entity { action } => cmd_entity(action),
        Commands::Finding { command } => match command {
            FindingCommands::Add {
                frontier,
                assertion,
                r#type,
                source,
                source_type,
                author,
                confidence,
                evidence_type,
                entities,
                entities_reviewed,
                evidence_span,
                gap,
                negative_space,
                doi,
                pmid,
                year,
                journal,
                url,
                source_authors,
                conditions_text,
                species,
                in_vivo,
                in_vitro,
                human_data,
                clinical_trial,
                json,
                apply,
            } => {
                validate_enum_arg("--type", &r#type, bundle::VALID_ASSERTION_TYPES);
                validate_enum_arg(
                    "--evidence-type",
                    &evidence_type,
                    bundle::VALID_EVIDENCE_TYPES,
                );
                validate_enum_arg(
                    "--source-type",
                    &source_type,
                    bundle::VALID_PROVENANCE_SOURCE_TYPES,
                );
                let parsed_entities = parse_entities(&entities);
                let parsed_evidence_spans = parse_evidence_spans(&evidence_span);
                for (name, etype) in &parsed_entities {
                    if !bundle::VALID_ENTITY_TYPES.contains(&etype.as_str()) {
                        fail(&format!(
                            "invalid entity type '{}' for '{}'. Valid: {}",
                            etype,
                            name,
                            bundle::VALID_ENTITY_TYPES.join(", "),
                        ));
                    }
                }
                let parsed_source_authors = source_authors
                    .map(|s| {
                        s.split(';')
                            .map(|a| a.trim().to_string())
                            .filter(|a| !a.is_empty())
                            .collect()
                    })
                    .unwrap_or_default();
                let parsed_species = species
                    .map(|s| {
                        s.split(';')
                            .map(|a| a.trim().to_string())
                            .filter(|a| !a.is_empty())
                            .collect()
                    })
                    .unwrap_or_default();
                let report = state::add_finding(
                    &frontier,
                    state::FindingDraftOptions {
                        text: assertion,
                        assertion_type: r#type,
                        source,
                        source_type,
                        author,
                        confidence,
                        evidence_type,
                        entities: parsed_entities,
                        doi,
                        pmid,
                        year,
                        journal,
                        url,
                        source_authors: parsed_source_authors,
                        conditions_text,
                        species: parsed_species,
                        in_vivo,
                        in_vitro,
                        human_data,
                        clinical_trial,
                        entities_reviewed,
                        evidence_spans: parsed_evidence_spans,
                        gap,
                        negative_space,
                    },
                    apply,
                )
                .unwrap_or_else(|e| fail_return(&e));
                print_state_report(&report, json);
            }
            FindingCommands::Supersede {
                frontier,
                old_id,
                assertion,
                r#type,
                source,
                source_type,
                author,
                reason,
                confidence,
                evidence_type,
                entities,
                doi,
                pmid,
                year,
                journal,
                url,
                source_authors,
                conditions_text,
                species,
                in_vivo,
                in_vitro,
                human_data,
                clinical_trial,
                json,
                apply,
            } => {
                validate_enum_arg("--type", &r#type, bundle::VALID_ASSERTION_TYPES);
                validate_enum_arg(
                    "--evidence-type",
                    &evidence_type,
                    bundle::VALID_EVIDENCE_TYPES,
                );
                validate_enum_arg(
                    "--source-type",
                    &source_type,
                    bundle::VALID_PROVENANCE_SOURCE_TYPES,
                );
                let parsed_entities = parse_entities(&entities);
                for (name, etype) in &parsed_entities {
                    if !bundle::VALID_ENTITY_TYPES.contains(&etype.as_str()) {
                        fail(&format!(
                            "invalid entity type '{}' for '{}'. Valid: {}",
                            etype,
                            name,
                            bundle::VALID_ENTITY_TYPES.join(", "),
                        ));
                    }
                }
                let parsed_source_authors = source_authors
                    .map(|s| {
                        s.split(';')
                            .map(|a| a.trim().to_string())
                            .filter(|a| !a.is_empty())
                            .collect()
                    })
                    .unwrap_or_default();
                let parsed_species = species
                    .map(|s| {
                        s.split(';')
                            .map(|a| a.trim().to_string())
                            .filter(|a| !a.is_empty())
                            .collect()
                    })
                    .unwrap_or_default();
                let report = state::supersede_finding(
                    &frontier,
                    &old_id,
                    &reason,
                    state::FindingDraftOptions {
                        text: assertion,
                        assertion_type: r#type,
                        source,
                        source_type,
                        author,
                        confidence,
                        evidence_type,
                        entities: parsed_entities,
                        doi,
                        pmid,
                        year,
                        journal,
                        url,
                        source_authors: parsed_source_authors,
                        conditions_text,
                        species: parsed_species,
                        in_vivo,
                        in_vitro,
                        human_data,
                        clinical_trial,
                        entities_reviewed: false,
                        evidence_spans: Vec::new(),
                        gap: false,
                        negative_space: false,
                    },
                    apply,
                )
                .unwrap_or_else(|e| fail_return(&e));
                print_state_report(&report, json);
            }
            FindingCommands::CausalSet {
                frontier,
                finding_id,
                claim,
                grade,
                actor,
                reason,
                json,
            } => {
                if !bundle::VALID_CAUSAL_CLAIMS.contains(&claim.as_str()) {
                    fail(&format!(
                        "invalid --claim '{claim}'; valid: {:?}",
                        bundle::VALID_CAUSAL_CLAIMS
                    ));
                }
                if let Some(g) = grade.as_deref()
                    && !bundle::VALID_CAUSAL_EVIDENCE_GRADES.contains(&g)
                {
                    fail(&format!(
                        "invalid --grade '{g}'; valid: {:?}",
                        bundle::VALID_CAUSAL_EVIDENCE_GRADES
                    ));
                }
                let report = state::set_causal(
                    &frontier,
                    &finding_id,
                    &claim,
                    grade.as_deref(),
                    &actor,
                    &reason,
                )
                .unwrap_or_else(|e| fail_return(&e));
                print_state_report(&report, json);
            }
        },
        Commands::Review {
            frontier,
            finding_id,
            status,
            reason,
            reviewer,
            apply,
            json,
        } => {
            let status = status.unwrap_or_else(|| fail_return("--status is required for review"));
            let reason = reason.unwrap_or_else(|| fail_return("--reason is required for review"));
            let report = state::review_finding(
                &frontier,
                &finding_id,
                state::ReviewOptions {
                    status,
                    reason,
                    reviewer,
                },
                apply,
            )
            .unwrap_or_else(|e| fail_return(&e));
            print_state_report(&report, json);
        }
        Commands::Note {
            frontier,
            finding_id,
            text,
            author,
            apply,
            json,
        } => {
            let report = state::add_note(&frontier, &finding_id, &text, &author, apply)
                .unwrap_or_else(|e| fail_return(&e));
            print_state_report(&report, json);
        }
        Commands::Caveat {
            frontier,
            finding_id,
            text,
            author,
            apply,
            json,
        } => {
            let report = state::caveat_finding(&frontier, &finding_id, &text, &author, apply)
                .unwrap_or_else(|e| fail_return(&e));
            print_state_report(&report, json);
        }
        Commands::Revise {
            frontier,
            finding_id,
            confidence,
            reason,
            reviewer,
            apply,
            json,
        } => {
            let report = state::revise_confidence(
                &frontier,
                &finding_id,
                state::ReviseOptions {
                    confidence,
                    reason,
                    reviewer,
                },
                apply,
            )
            .unwrap_or_else(|e| fail_return(&e));
            print_state_report(&report, json);
        }
        Commands::Reject {
            frontier,
            finding_id,
            reason,
            reviewer,
            apply,
            json,
        } => {
            let report = state::reject_finding(&frontier, &finding_id, &reviewer, &reason, apply)
                .unwrap_or_else(|e| fail_return(&e));
            print_state_report(&report, json);
        }
        Commands::History {
            frontier,
            finding_id,
            json,
            as_of,
        } => {
            let payload = state::history_as_of(&frontier, &finding_id, as_of.as_deref())
                .unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize history response")
                );
            } else {
                print_history(&payload);
            }
        }
        Commands::ImportEvents { source, into, json } => {
            let report =
                review::import_review_events(&source, &into).unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "import-events",
                        "source": report.source,
                        "target": into.display().to_string(),
                        "summary": {
                            "imported": report.imported,
                            "new": report.new,
                            "duplicate": report.duplicate,
                            "canonical_events_imported": report.events_imported,
                            "canonical_events_new": report.events_new,
                            "canonical_events_duplicate": report.events_duplicate,
                        }
                    }))
                    .expect("failed to serialize import-events response")
                );
            } else {
                println!("{report}");
            }
        }
        Commands::Retract {
            source,
            finding_id,
            reason,
            reviewer,
            apply,
            json,
        } => {
            let report = state::retract_finding(&source, &finding_id, &reviewer, &reason, apply)
                .unwrap_or_else(|e| fail_return(&e));
            print_state_report(&report, json);
        }
        Commands::LocatorRepair {
            frontier,
            atom_id,
            locator,
            reviewer,
            reason,
            apply,
            json,
        } => {
            cmd_locator_repair(
                &frontier,
                &atom_id,
                locator.as_deref(),
                &reviewer,
                &reason,
                apply,
                json,
            );
        }
        Commands::SourceFetch {
            identifier,
            cache,
            out,
            refresh,
            json,
        } => {
            cmd_source_fetch(&identifier, cache.as_deref(), out.as_deref(), refresh, json).await;
        }
        Commands::SpanRepair {
            frontier,
            finding_id,
            section,
            text,
            reviewer,
            reason,
            apply,
            json,
        } => {
            cmd_span_repair(
                &frontier,
                &finding_id,
                &section,
                &text,
                &reviewer,
                &reason,
                apply,
                json,
            );
        }
        Commands::EntityAdd {
            frontier,
            finding_id,
            entity,
            entity_type,
            reviewer,
            reason,
            apply,
            json,
        } => {
            let report = state::add_finding_entity(
                &frontier,
                &finding_id,
                &entity,
                &entity_type,
                &reviewer,
                &reason,
                apply,
            )
            .unwrap_or_else(|e| fail_return(&e));
            print_state_report(&report, json);
        }
        Commands::EntityResolve {
            frontier,
            finding_id,
            entity,
            source,
            id,
            confidence,
            matched_name,
            resolution_method,
            reviewer,
            reason,
            apply,
            json,
        } => {
            cmd_entity_resolve(
                &frontier,
                &finding_id,
                &entity,
                &source,
                &id,
                confidence,
                matched_name.as_deref(),
                &resolution_method,
                &reviewer,
                &reason,
                apply,
                json,
            );
        }
        Commands::Propagate {
            frontier,
            retract,
            reduce_confidence,
            to,
            output,
        } => cmd_propagate(&frontier, retract, reduce_confidence, to, output.as_deref()),
        Commands::Replicate {
            frontier,
            target,
            outcome,
            by,
            conditions,
            source_title,
            doi,
            pmid,
            sample_size,
            note,
            previous_attempt,
            no_cascade,
            json,
        } => cmd_replicate(
            &frontier,
            &target,
            &outcome,
            &by,
            &conditions,
            &source_title,
            doi.as_deref(),
            pmid.as_deref(),
            sample_size.as_deref(),
            &note,
            previous_attempt.as_deref(),
            no_cascade,
            json,
        ),
        Commands::Replications {
            frontier,
            target,
            json,
        } => cmd_replications(&frontier, target.as_deref(), json),
        Commands::DatasetAdd {
            frontier,
            name,
            version,
            content_hash,
            url,
            license,
            source_title,
            doi,
            row_count,
            json,
        } => cmd_dataset_add(
            &frontier,
            &name,
            version.as_deref(),
            &content_hash,
            url.as_deref(),
            license.as_deref(),
            &source_title,
            doi.as_deref(),
            row_count,
            json,
        ),
        Commands::Datasets { frontier, json } => cmd_datasets(&frontier, json),
        Commands::CodeAdd {
            frontier,
            language,
            repo_url,
            commit,
            path,
            content_hash,
            line_start,
            line_end,
            entry_point,
            json,
        } => cmd_code_add(
            &frontier,
            &language,
            repo_url.as_deref(),
            commit.as_deref(),
            &path,
            &content_hash,
            line_start,
            line_end,
            entry_point.as_deref(),
            json,
        ),
        Commands::CodeArtifacts { frontier, json } => cmd_code_artifacts(&frontier, json),
        Commands::ArtifactAdd {
            frontier,
            kind,
            name,
            file,
            url,
            content_hash,
            media_type,
            license,
            source_title,
            source_url,
            doi,
            target,
            metadata,
            access_tier,
            deposited_by,
            reason,
            json,
        } => cmd_artifact_add(
            &frontier,
            &kind,
            &name,
            file.as_deref(),
            url.as_deref(),
            content_hash.as_deref(),
            media_type.as_deref(),
            license.as_deref(),
            source_title.as_deref(),
            source_url.as_deref(),
            doi.as_deref(),
            target,
            metadata,
            &access_tier,
            &deposited_by,
            &reason,
            json,
        ),
        Commands::Artifacts {
            frontier,
            target,
            json,
        } => cmd_artifacts(&frontier, target.as_deref(), json),
        Commands::ArtifactAudit { frontier, json } => cmd_artifact_audit(&frontier, json),
        Commands::DecisionBrief { frontier, json } => cmd_decision_brief(&frontier, json),
        Commands::TrialSummary { frontier, json } => cmd_trial_summary(&frontier, json),
        Commands::SourceVerification { frontier, json } => cmd_source_verification(&frontier, json),
        Commands::SourceIngestPlan { frontier, json } => cmd_source_ingest_plan(&frontier, json),
        Commands::ClinicalTrialImport {
            frontier,
            nct_id,
            input_json,
            target,
            deposited_by,
            reason,
            license,
            json,
        } => {
            cmd_clinical_trial_import(
                &frontier,
                &nct_id,
                input_json.as_deref(),
                target,
                &deposited_by,
                &reason,
                &license,
                json,
            )
            .await
        }
        Commands::NegativeResultAdd {
            frontier,
            kind,
            deposited_by,
            reason,
            conditions_text,
            notes,
            target,
            endpoint,
            intervention,
            comparator,
            population,
            n_enrolled,
            power,
            ci_lower,
            ci_upper,
            effect_size_threshold,
            registry_id,
            reagent,
            observation,
            attempts,
            source_title,
            doi,
            url,
            year,
            json,
        } => cmd_negative_result_add(
            &frontier,
            &kind,
            &deposited_by,
            &reason,
            &conditions_text,
            &notes,
            target,
            endpoint.as_deref(),
            intervention.as_deref(),
            comparator.as_deref(),
            population.as_deref(),
            n_enrolled,
            power,
            ci_lower,
            ci_upper,
            effect_size_threshold,
            registry_id.as_deref(),
            reagent.as_deref(),
            observation.as_deref(),
            attempts,
            &source_title,
            doi.as_deref(),
            url.as_deref(),
            year,
            json,
        ),
        Commands::NegativeResults {
            frontier,
            target,
            json,
        } => cmd_negative_results(&frontier, target.as_deref(), json),
        Commands::TrajectoryCreate {
            frontier,
            deposited_by,
            reason,
            target,
            notes,
            json,
        } => cmd_trajectory_create(&frontier, &deposited_by, &reason, target, &notes, json),
        Commands::TrajectoryStep {
            frontier,
            trajectory_id,
            kind,
            description,
            actor,
            reason,
            reference,
            json,
        } => cmd_trajectory_step(
            &frontier,
            &trajectory_id,
            &kind,
            &description,
            &actor,
            &reason,
            reference,
            json,
        ),
        Commands::Trajectories {
            frontier,
            target,
            json,
        } => cmd_trajectories(&frontier, target.as_deref(), json),
        Commands::TierSet {
            frontier,
            object_type,
            object_id,
            tier,
            actor,
            reason,
            json,
        } => cmd_tier_set(
            &frontier,
            &object_type,
            &object_id,
            &tier,
            &actor,
            &reason,
            json,
        ),
        Commands::Predict {
            frontier,
            by,
            claim,
            criterion,
            resolves_by,
            confidence,
            target,
            outcome,
            conditions,
            json,
        } => cmd_predict(
            &frontier,
            &by,
            &claim,
            &criterion,
            resolves_by.as_deref(),
            confidence,
            &target,
            &outcome,
            &conditions,
            json,
        ),
        Commands::Resolve {
            frontier,
            prediction,
            outcome,
            matched,
            by,
            confidence,
            source_title,
            doi,
            json,
        } => cmd_resolve(
            &frontier,
            &prediction,
            &outcome,
            matched,
            &by,
            confidence,
            &source_title,
            doi.as_deref(),
            json,
        ),
        Commands::Predictions {
            frontier,
            by,
            open,
            json,
        } => cmd_predictions(&frontier, by.as_deref(), open, json),
        Commands::Calibration {
            frontier,
            actor,
            json,
        } => cmd_calibration(&frontier, actor.as_deref(), json),
        Commands::PredictionsExpire {
            frontier,
            now,
            dry_run,
            json,
        } => cmd_predictions_expire(&frontier, now.as_deref(), dry_run, json),
        Commands::Consensus {
            frontier,
            target,
            weighting,
            causal_claim,
            causal_grade_min,
            json,
        } => cmd_consensus(
            &frontier,
            &target,
            &weighting,
            causal_claim.as_deref(),
            causal_grade_min.as_deref(),
            json,
        ),

        // v0.74: alias verb dispatch. Each arm calls into an
        // existing canonical-event emission path.
        Commands::Ingest {
            path,
            frontier,
            backend,
            actor,
            dry_run,
            json,
        } => {
            cmd_ingest(
                &path,
                &frontier,
                backend.as_deref(),
                actor.as_deref(),
                dry_run,
                json,
            )
            .await
        }

        Commands::Propose {
            frontier,
            finding_id,
            status,
            reason,
            reviewer,
            apply,
            json,
        } => {
            // Mirror the existing `Commands::Review` arm: emit a
            // finding.review proposal under reviewer authority.
            let options = state::ReviewOptions {
                status: status.clone(),
                reason: reason.clone(),
                reviewer: reviewer.clone(),
            };
            let report = state::review_finding(&frontier, &finding_id, options, apply)
                .unwrap_or_else(|e| fail_return(&e));
            print_state_report(&report, json);
        }

        Commands::Accept {
            frontier,
            proposal_id,
            reviewer,
            reason,
            json,
        } => {
            // Mirror ProposalAction::Accept at cli.rs:8000.
            let event_id = proposals::accept_at_path(&frontier, &proposal_id, &reviewer, &reason)
                .unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "accept",
                "frontier": frontier.display().to_string(),
                "proposal_id": proposal_id,
                "reviewer": reviewer,
                "applied_event_id": event_id,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize accept response")
                );
            } else {
                println!(
                    "{} accepted and applied proposal {}",
                    style::ok("ok"),
                    proposal_id
                );
                println!("  event: {}", event_id);
            }
        }

        Commands::Attest {
            frontier,
            event,
            attester,
            scope_note,
            proof_id,
            signature,
            key,
            json,
        } => {
            // v0.80.1: per-event mode. When --event is supplied,
            // emit an attestation.recorded canonical event
            // targeting the named event id.
            if let Some(target_event_id) = event {
                let attester_id = attester.unwrap_or_else(|| {
                    fail_return("attest: --attester is required in per-event mode")
                });
                let scope = scope_note.unwrap_or_else(|| {
                    fail_return("attest: --scope-note is required in per-event mode")
                });
                let attestation_event_id = state::record_attestation(
                    &frontier,
                    &target_event_id,
                    &attester_id,
                    &scope,
                    proof_id.as_deref(),
                    signature.as_deref(),
                )
                .unwrap_or_else(|e| fail_return(&e));
                if json {
                    let payload = json!({
                        "ok": true,
                        "command": "attest.event",
                        "frontier": frontier.display().to_string(),
                        "target_event_id": target_event_id,
                        "attestation_event_id": attestation_event_id,
                        "attester_id": attester_id,
                    });
                    println!(
                        "{}",
                        serde_json::to_string_pretty(&payload)
                            .expect("failed to serialize attest.event response")
                    );
                } else {
                    println!(
                        "{} attested {} by {} ({})",
                        style::ok("ok"),
                        target_event_id,
                        attester_id,
                        attestation_event_id
                    );
                }
                return;
            }
            // v0.74 frontier-wide path: --key required.
            let key_path = key.unwrap_or_else(|| {
                fail_return(
                    "attest: --key is required in frontier-wide mode (or pass --event for per-event mode)",
                )
            });
            let count =
                sign::sign_frontier(&frontier, &key_path).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "attest",
                "frontier": frontier.display().to_string(),
                "private_key": key_path.display().to_string(),
                "signed": count,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize attest response")
                );
            } else {
                println!(
                    "{} {count} findings in {}",
                    style::ok("attested"),
                    frontier.display()
                );
            }
        }

        Commands::Lineage {
            frontier,
            finding_id,
            as_of,
            json,
        } => {
            // Mirror Commands::History at cli.rs:3231.
            let payload = state::history_as_of(&frontier, &finding_id, as_of.as_deref())
                .unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize lineage response")
                );
            } else {
                print_history(&payload);
            }
        }

        Commands::Carina { action } => cmd_carina(action),

        Commands::Atlas { action } => cmd_atlas(action).await,

        Commands::Constellation { action } => cmd_constellation(action).await,
    }
}

/// v0.78: handler for `vela atlas <action>`. Routes through the
/// binary-installed handlers (registered in `vela-cli/src/main.rs`)
/// so the substrate library stays free of the `vela-atlas`
/// dependency.
async fn cmd_atlas(action: AtlasAction) {
    match action {
        AtlasAction::Init {
            name,
            frontiers,
            domain,
            scope_note,
            atlases_root,
            json,
        } => match ATLAS_INIT_HANDLER.get() {
            Some(handler) => {
                handler(atlases_root, name, domain, scope_note, frontiers, json).await;
            }
            None => fail("vela atlas init: handler not registered (built without vela-atlas)"),
        },
        AtlasAction::Materialize {
            name,
            atlases_root,
            json,
        } => match ATLAS_MATERIALIZE_HANDLER.get() {
            Some(handler) => handler(atlases_root, name, json).await,
            None => fail("vela atlas materialize: handler not registered"),
        },
        AtlasAction::Serve {
            name,
            atlases_root,
            port,
            no_open,
        } => {
            // v0.78 stub: route to the per-frontier Workbench for
            // the first composing frontier in the manifest.
            // Atlas-level Workbench page lands in v0.79+.
            match ATLAS_SERVE_HANDLER.get() {
                Some(handler) => handler(atlases_root, name, port, !no_open).await,
                None => fail("vela atlas serve: handler not registered"),
            }
        }
        AtlasAction::Update {
            name,
            add_frontier,
            remove_vfr_id,
            atlases_root,
            json,
        } => match ATLAS_UPDATE_HANDLER.get() {
            Some(handler) => {
                handler(atlases_root, name, add_frontier, remove_vfr_id, json).await;
            }
            None => fail("vela atlas update: handler not registered"),
        },
    }
}

/// v0.82: handler for `vela constellation <action>`. Routes
/// through binary-installed handlers calling into the
/// `vela-constellation` crate.
async fn cmd_constellation(action: ConstellationAction) {
    match action {
        ConstellationAction::Init {
            name,
            atlases,
            scope_note,
            constellations_root,
            json,
        } => match CONSTELLATION_INIT_HANDLER.get() {
            Some(handler) => {
                handler(constellations_root, name, scope_note, atlases, json).await;
            }
            None => fail(
                "vela constellation init: handler not registered (built without vela-constellation)",
            ),
        },
        ConstellationAction::Materialize {
            name,
            constellations_root,
            json,
        } => match CONSTELLATION_MATERIALIZE_HANDLER.get() {
            Some(handler) => handler(constellations_root, name, json).await,
            None => fail("vela constellation materialize: handler not registered"),
        },
        ConstellationAction::Serve {
            name,
            constellations_root,
            port,
            no_open,
        } => match CONSTELLATION_SERVE_HANDLER.get() {
            Some(handler) => handler(constellations_root, name, port, !no_open).await,
            None => fail("vela constellation serve: handler not registered"),
        },
    }
}

/// v0.75: handler for `vela carina <action>`. Each branch reaches
/// into the bundled schemas under `embedded/carina-schemas/`.
fn cmd_carina(action: CarinaAction) {
    match action {
        CarinaAction::List { json } => {
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "carina.list",
                        "primitives": carina_validate::PRIMITIVE_NAMES,
                    }))
                    .expect("failed to serialize carina.list")
                );
            } else {
                println!("Carina primitives bundled with this build:");
                for name in carina_validate::PRIMITIVE_NAMES {
                    println!("  · {name}");
                }
            }
        }
        CarinaAction::Schema { primitive } => match carina_validate::schema_text(&primitive) {
            Some(text) => print!("{text}"),
            None => fail(&format!("carina: unknown primitive '{primitive}'")),
        },
        CarinaAction::Validate {
            path,
            primitive,
            json,
        } => {
            let text = std::fs::read_to_string(&path)
                .unwrap_or_else(|e| fail_return(&format!("read {}: {e}", path.display())));
            let value: Value = serde_json::from_str(&text)
                .unwrap_or_else(|e| fail_return(&format!("parse {}: {e}", path.display())));
            // If the file is a primitives.v0.X.json aggregate,
            // validate every entry under `primitives`. Otherwise
            // validate the value as one primitive.
            // Each report entry: (input key, validation result with
            // optional detected-primitive name in the Ok branch).
            type CarinaValidateOutcome = Result<Option<&'static str>, Vec<String>>;
            let mut report: Vec<(String, CarinaValidateOutcome)> = Vec::new();
            if value.get("primitives").and_then(Value::as_object).is_some() && primitive.is_none() {
                let primitives = value.get("primitives").and_then(Value::as_object).unwrap();
                for (key, child) in primitives {
                    let outcome = carina_validate::validate(key, child)
                        .map(|()| carina_validate::detect_primitive(child));
                    report.push((key.clone(), outcome));
                }
            } else {
                let outcome = match primitive.as_deref() {
                    Some(name) => carina_validate::validate(name, &value).map(|()| {
                        carina_validate::PRIMITIVE_NAMES
                            .iter()
                            .copied()
                            .find(|p| *p == name)
                    }),
                    None => carina_validate::validate_auto(&value).map(Some),
                };
                let label = primitive.clone().unwrap_or_else(|| "<auto>".to_string());
                report.push((label, outcome));
            }

            let total = report.len();
            let pass = report.iter().filter(|(_, r)| r.is_ok()).count();
            let fail = total - pass;

            if json {
                let entries: Vec<Value> = report
                    .iter()
                    .map(|(label, r)| match r {
                        Ok(name) => json!({
                            "key": label,
                            "primitive": name,
                            "ok": true,
                        }),
                        Err(errs) => json!({
                            "key": label,
                            "ok": false,
                            "errors": errs,
                        }),
                    })
                    .collect();
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": fail == 0,
                        "command": "carina.validate",
                        "file": path.display().to_string(),
                        "total": total,
                        "passed": pass,
                        "failed": fail,
                        "entries": entries,
                    }))
                    .expect("failed to serialize carina.validate")
                );
            } else {
                for (label, r) in &report {
                    match r {
                        Ok(Some(name)) => println!("  {} {label} (as {name})", style::ok("ok")),
                        Ok(None) => println!("  {} {label}", style::ok("ok")),
                        Err(errs) => {
                            println!("  {} {label}", style::lost("fail"));
                            for e in errs {
                                println!("      {e}");
                            }
                        }
                    }
                }
                println!();
                if fail == 0 {
                    println!("{} {pass}/{total} valid", style::ok("carina.validate"));
                } else {
                    println!(
                        "{} {pass}/{total} valid · {fail} failed",
                        style::lost("carina.validate")
                    );
                }
            }

            if fail > 0 {
                std::process::exit(1);
            }
        }
    }
}

/// v0.35 / v0.38.2: print consensus over claim-similar findings,
/// optionally filtered by causal claim type / minimum study grade.
fn cmd_consensus(
    frontier: &Path,
    target: &str,
    weighting_str: &str,
    causal_claim: Option<&str>,
    causal_grade_min: Option<&str>,
    json: bool,
) {
    use crate::bundle::{CausalClaim, CausalEvidenceGrade};

    if !target.starts_with("vf_") {
        fail(&format!("target `{target}` is not a vf_ finding id"));
    }
    let scheme =
        crate::aggregate::WeightingScheme::parse(weighting_str).unwrap_or_else(|e| fail_return(&e));

    let parsed_claim = match causal_claim {
        None => None,
        Some("correlation") => Some(CausalClaim::Correlation),
        Some("mediation") => Some(CausalClaim::Mediation),
        Some("intervention") => Some(CausalClaim::Intervention),
        Some(other) => fail_return(&format!(
            "invalid --causal-claim '{other}'; valid: correlation | mediation | intervention"
        )),
    };
    let parsed_grade = match causal_grade_min {
        None => None,
        Some("theoretical") => Some(CausalEvidenceGrade::Theoretical),
        Some("observational") => Some(CausalEvidenceGrade::Observational),
        Some("quasi_experimental") => Some(CausalEvidenceGrade::QuasiExperimental),
        Some("rct") => Some(CausalEvidenceGrade::Rct),
        Some(other) => fail_return(&format!(
            "invalid --causal-grade-min '{other}'; valid: theoretical | observational | quasi_experimental | rct"
        )),
    };
    let filter = crate::aggregate::AggregateFilter {
        causal_claim: parsed_claim,
        causal_grade_min: parsed_grade,
    };
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));

    let result = crate::aggregate::consensus_for_with_filter(&project, target, scheme, &filter)
        .unwrap_or_else(|| fail_return(&format!("target `{target}` not in frontier")));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&result).expect("serialize consensus")
        );
        return;
    }

    println!();
    println!(
        "  {}",
        format!(
            "VELA · CONSENSUS · {} ({})",
            result.target, result.weighting
        )
        .to_uppercase()
        .dimmed()
    );
    println!("  {}", style::tick_row(60));
    println!(
        "  target:           {}",
        truncate(&result.target_assertion, 80)
    );
    println!("  similar findings: {}", result.n_findings);
    println!(
        "  consensus:        {:.3}  ({:.3} – {:.3} 95% credible)",
        result.consensus_confidence, result.credible_interval_lo, result.credible_interval_hi
    );
    println!();
    println!("  constituents (sorted by weight):");
    let mut sorted = result.constituents.clone();
    sorted.sort_by(|a, b| {
        b.weight
            .partial_cmp(&a.weight)
            .unwrap_or(std::cmp::Ordering::Equal)
    });
    for c in sorted.iter().take(10) {
        let repls = if c.n_replications > 0 {
            format!("  ({}r {}f)", c.n_replicated, c.n_failed_replications)
        } else {
            String::new()
        };
        println!(
            "    · w={:.2}  raw={:.2}  adj={:.2}{}",
            c.weight, c.raw_score, c.adjusted_score, repls
        );
        println!("        {}", truncate(&c.assertion_text, 88));
    }
    if result.constituents.len() > 10 {
        println!("    ... ({} more)", result.constituents.len() - 10);
    }
}

/// v0.34: parse the `--outcome` CLI string into a structured
/// `ExpectedOutcome`. Accepted forms:
///   - `affirmed` / `falsified`
///   - `quant:VALUE±TOL UNITS`  (e.g. `quant:0.4±0.1 SD`)
///   - `cat:LABEL`              (e.g. `cat:full_approval`)
fn parse_expected_outcome(s: &str) -> Result<crate::bundle::ExpectedOutcome, String> {
    let trimmed = s.trim();
    if trimmed.eq_ignore_ascii_case("affirmed") {
        return Ok(crate::bundle::ExpectedOutcome::Affirmed);
    }
    if trimmed.eq_ignore_ascii_case("falsified") {
        return Ok(crate::bundle::ExpectedOutcome::Falsified);
    }
    if let Some(rest) = trimmed.strip_prefix("cat:") {
        return Ok(crate::bundle::ExpectedOutcome::Categorical {
            value: rest.to_string(),
        });
    }
    if let Some(rest) = trimmed.strip_prefix("quant:") {
        let (vt, units) = rest.split_once(' ').unwrap_or((rest, ""));
        let (val_s, tol_s) = vt
            .split_once('±')
            .or_else(|| vt.split_once("+/-"))
            .ok_or_else(|| format!("expected `quant:VALUE±TOL UNITS`, got `quant:{rest}`"))?;
        let value: f64 = val_s
            .parse()
            .map_err(|e| format!("bad quant value `{val_s}`: {e}"))?;
        let tolerance: f64 = tol_s
            .parse()
            .map_err(|e| format!("bad quant tolerance `{tol_s}`: {e}"))?;
        return Ok(crate::bundle::ExpectedOutcome::Quantitative {
            value,
            tolerance,
            units: units.to_string(),
        });
    }
    Err(format!(
        "unknown outcome `{s}`; expected one of: affirmed | falsified | quant:V±T units | cat:label"
    ))
}

/// v0.34: append a Prediction to a frontier and persist it.
#[allow(clippy::too_many_arguments)]
fn cmd_predict(
    frontier: &Path,
    by: &str,
    claim: &str,
    criterion: &str,
    resolves_by: Option<&str>,
    confidence: f64,
    target_csv: &str,
    outcome: &str,
    conditions_text: &str,
    json: bool,
) {
    if !(0.0..=1.0).contains(&confidence) {
        fail(&format!("confidence must be in [0, 1]; got {confidence}"));
    }
    let expected = parse_expected_outcome(outcome).unwrap_or_else(|e| fail_return(&e));

    let mut project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));

    let targets: Vec<String> = target_csv
        .split(',')
        .map(|s| s.trim().to_string())
        .filter(|s| !s.is_empty())
        .collect();
    for t in &targets {
        if !t.starts_with("vf_") {
            fail(&format!("target `{t}` is not a vf_ id"));
        }
        if !project.findings.iter().any(|f| f.id == *t) {
            fail(&format!("target `{t}` not present in frontier"));
        }
    }

    let lower = conditions_text.to_lowercase();
    let conditions = crate::bundle::Conditions {
        text: conditions_text.to_string(),
        species_verified: Vec::new(),
        species_unverified: Vec::new(),
        in_vitro: lower.contains("in vitro"),
        in_vivo: lower.contains("in vivo"),
        human_data: lower.contains("human") || lower.contains("clinical"),
        clinical_trial: lower.contains("clinical trial") || lower.contains("phase "),
        concentration_range: None,
        duration: None,
        age_group: None,
        cell_type: None,
    };

    let prediction = crate::bundle::Prediction::new(
        claim.to_string(),
        targets,
        None,
        resolves_by.map(|s| s.to_string()),
        criterion.to_string(),
        expected,
        by.to_string(),
        confidence,
        conditions,
    );

    if project.predictions.iter().any(|p| p.id == prediction.id) {
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "ok": false,
                    "command": "predict",
                    "reason": "prediction_already_exists",
                    "id": prediction.id,
                }))
                .expect("serialize")
            );
        } else {
            println!(
                "{} prediction {} already exists in {}; skipping.",
                style::warn("predict"),
                prediction.id,
                frontier.display()
            );
        }
        return;
    }

    let new_id = prediction.id.clone();
    project.predictions.push(prediction);
    repo::save_to_path(frontier, &project).unwrap_or_else(|e| fail_return(&e));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "predict",
                "id": new_id,
                "made_by": by,
                "confidence": confidence,
                "frontier": frontier.display().to_string(),
            }))
            .expect("serialize predict result")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · PREDICT · {}", new_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  by:           {by}");
        println!("  confidence:   {confidence:.3}");
        if let Some(d) = resolves_by {
            println!("  resolves by:  {d}");
        }
        println!("  outcome:      {outcome}");
        println!("  claim:        {}", truncate(claim, 88));
        println!();
        println!(
            "  {} prediction recorded in {}",
            style::ok("ok"),
            frontier.display()
        );
    }
}

/// v0.34: append a Resolution that closes out a Prediction.
#[allow(clippy::too_many_arguments)]
fn cmd_resolve(
    frontier: &Path,
    prediction_id: &str,
    actual_outcome: &str,
    matched: bool,
    by: &str,
    confidence: f64,
    source_title: &str,
    doi: Option<&str>,
    json: bool,
) {
    if !prediction_id.starts_with("vpred_") {
        fail(&format!("prediction `{prediction_id}` is not a vpred_ id"));
    }
    if !(0.0..=1.0).contains(&confidence) {
        fail(&format!("confidence must be in [0, 1]; got {confidence}"));
    }
    let mut project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    if !project.predictions.iter().any(|p| p.id == prediction_id) {
        fail(&format!(
            "prediction `{prediction_id}` not present in frontier"
        ));
    }

    let evidence = crate::bundle::Evidence {
        evidence_type: "experimental".to_string(),
        model_system: String::new(),
        species: None,
        method: "prediction_resolution".to_string(),
        sample_size: None,
        effect_size: None,
        p_value: None,
        replicated: false,
        replication_count: None,
        evidence_spans: if source_title.is_empty() {
            Vec::new()
        } else {
            vec![serde_json::json!({"text": source_title})]
        },
    };

    // If the resolver provided source provenance, embed it via the
    // evidence span (the Resolution carries Evidence; for v0.34 we
    // keep the structure minimal). DOI flows through evidence_spans
    // commentary; richer linking lands in v0.34.x.
    let _ = doi; // currently unused — placeholder for v0.34.x.

    let resolution = crate::bundle::Resolution::new(
        prediction_id.to_string(),
        actual_outcome.to_string(),
        matched,
        by.to_string(),
        evidence,
        confidence,
    );

    if project.resolutions.iter().any(|r| r.id == resolution.id) {
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "ok": false,
                    "command": "resolve",
                    "reason": "resolution_already_exists",
                    "id": resolution.id,
                }))
                .expect("serialize")
            );
        } else {
            println!(
                "{} resolution {} already exists in {}; skipping.",
                style::warn("resolve"),
                resolution.id,
                frontier.display()
            );
        }
        return;
    }

    let new_id = resolution.id.clone();
    project.resolutions.push(resolution);
    repo::save_to_path(frontier, &project).unwrap_or_else(|e| fail_return(&e));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "resolve",
                "id": new_id,
                "prediction": prediction_id,
                "matched": matched,
                "frontier": frontier.display().to_string(),
            }))
            .expect("serialize resolve result")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · RESOLVE · {}", new_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  prediction:   {prediction_id}");
        println!(
            "  matched:      {}",
            if matched {
                style::ok("yes")
            } else {
                style::lost("no")
            }
        );
        println!("  by:           {by}");
        println!("  outcome:      {}", truncate(actual_outcome, 80));
        println!();
        println!(
            "  {} resolution recorded in {}",
            style::ok("ok"),
            frontier.display()
        );
    }
}

/// v0.34: list predictions, with resolution state.
fn cmd_predictions(frontier: &Path, by: Option<&str>, open: bool, json: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));

    let resolved_ids: std::collections::HashSet<&str> = project
        .resolutions
        .iter()
        .map(|r| r.prediction_id.as_str())
        .collect();

    let mut filtered: Vec<&crate::bundle::Prediction> = project
        .predictions
        .iter()
        .filter(|p| by.is_none_or(|b| p.made_by == b))
        .filter(|p| !open || !resolved_ids.contains(p.id.as_str()))
        .collect();
    filtered.sort_by(|a, b| {
        a.resolves_by
            .as_deref()
            .unwrap_or("9999")
            .cmp(b.resolves_by.as_deref().unwrap_or("9999"))
    });

    if json {
        let payload: Vec<serde_json::Value> = filtered
            .iter()
            .map(|p| {
                json!({
                    "id": p.id,
                    "claim_text": p.claim_text,
                    "made_by": p.made_by,
                    "confidence": p.confidence,
                    "predicted_at": p.predicted_at,
                    "resolves_by": p.resolves_by,
                    "expected_outcome": p.expected_outcome,
                    "resolved": resolved_ids.contains(p.id.as_str()),
                })
            })
            .collect();
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "predictions",
                "frontier": frontier.display().to_string(),
                "count": payload.len(),
                "predictions": payload,
            }))
            .expect("serialize predictions")
        );
        return;
    }

    println!();
    println!(
        "  {}",
        format!("VELA · PREDICTIONS · {}", frontier.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if filtered.is_empty() {
        println!("  (no predictions matching filters)");
        return;
    }
    for p in &filtered {
        let resolved = resolved_ids.contains(p.id.as_str());
        let chip = if resolved {
            style::ok("resolved")
        } else {
            style::warn("open")
        };
        let deadline = p.resolves_by.as_deref().unwrap_or("(no deadline)");
        println!(
            "  · {}  {}  by {}  → {}",
            p.id.dimmed(),
            chip,
            p.made_by,
            deadline,
        );
        println!("      claim:      {}", truncate(&p.claim_text, 90));
        println!("      confidence: {:.2}", p.confidence);
    }
}

/// v0.34: print calibration scores per actor.
/// v0.40.1: Walk every prediction whose deadline has passed and mark
/// them as `expired_unresolved`. Emits one
/// `prediction.expired_unresolved` event per newly-expired prediction.
fn cmd_predictions_expire(frontier: &Path, now_override: Option<&str>, dry_run: bool, json: bool) {
    use chrono::DateTime;

    let now_dt = match now_override {
        Some(s) => DateTime::parse_from_rfc3339(s)
            .map(|dt| dt.with_timezone(&chrono::Utc))
            .unwrap_or_else(|e| fail_return(&format!("invalid --now '{s}': {e}"))),
        None => chrono::Utc::now(),
    };

    let mut project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    if dry_run {
        // Run on a clone so we don't actually mutate.
        let mut probe = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
        let report = crate::calibration::expire_overdue_predictions(&mut probe, now_dt);
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "ok": true,
                    "command": "predictions.expire",
                    "dry_run": true,
                    "report": report,
                }))
                .expect("serialize predictions.expire (dry-run)")
            );
        } else {
            println!(
                "{} dry-run @ {}: {} would expire, {} already expired, {} resolved, {} still open",
                style::ok("ok"),
                report.now,
                report.newly_expired.len(),
                report.already_expired.len(),
                report.already_resolved.len(),
                report.still_open.len(),
            );
            for id in &report.newly_expired {
                println!("  · {id}");
            }
        }
        return;
    }

    let report = crate::calibration::expire_overdue_predictions(&mut project, now_dt);
    repo::save_to_path(frontier, &project).unwrap_or_else(|e| fail_return(&e));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "predictions.expire",
                "report": report,
            }))
            .expect("serialize predictions.expire")
        );
    } else {
        println!(
            "{} @ {}: {} newly expired, {} already expired, {} resolved, {} still open",
            style::ok("expired"),
            report.now,
            report.newly_expired.len(),
            report.already_expired.len(),
            report.already_resolved.len(),
            report.still_open.len(),
        );
        for id in &report.newly_expired {
            println!("  · {id}");
        }
    }
}

fn cmd_calibration(frontier: &Path, actor: Option<&str>, json: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let records = match actor {
        Some(a) => {
            crate::calibration::calibration_for_actor(a, &project.predictions, &project.resolutions)
                .map(|r| vec![r])
                .unwrap_or_default()
        }
        None => crate::calibration::calibration_records(&project.predictions, &project.resolutions),
    };

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "calibration",
                "frontier": frontier.display().to_string(),
                "filter_actor": actor,
                "records": records,
            }))
            .expect("serialize calibration")
        );
        return;
    }

    println!();
    println!(
        "  {}",
        format!("VELA · CALIBRATION · {}", frontier.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if records.is_empty() {
        println!("  (no calibration records)");
        return;
    }
    for r in &records {
        println!("  · {}", r.actor);
        println!(
            "      predictions: {}  resolved: {}  hits: {}",
            r.n_predictions, r.n_resolved, r.n_hit
        );
        match r.hit_rate {
            Some(h) => println!("      hit rate:    {:.1}%", h * 100.0),
            None => println!("      hit rate:    n/a"),
        }
        match r.brier_score {
            Some(b) => println!(
                "      brier:       {:.4}  (lower is better; 0.25 = chance)",
                b
            ),
            None => println!("      brier:       n/a"),
        }
        match r.log_score {
            Some(l) => println!(
                "      log score:   {:.4}  (higher is better; 0 = perfect)",
                l
            ),
            None => println!("      log score:   n/a"),
        }
    }
}

/// v0.33: append a Dataset record to a frontier and persist it.
#[allow(clippy::too_many_arguments)]
fn cmd_dataset_add(
    frontier: &Path,
    name: &str,
    version: Option<&str>,
    content_hash: &str,
    url: Option<&str>,
    license: Option<&str>,
    source_title: &str,
    doi: Option<&str>,
    row_count: Option<u64>,
    json: bool,
) {
    let mut project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));

    let provenance = crate::bundle::Provenance {
        source_type: "data_release".to_string(),
        doi: doi.map(|s| s.to_string()),
        pmid: None,
        pmc: None,
        openalex_id: None,
        url: url.map(|s| s.to_string()),
        title: source_title.to_string(),
        authors: Vec::new(),
        year: None,
        journal: None,
        license: license.map(|s| s.to_string()),
        publisher: None,
        funders: Vec::new(),
        extraction: crate::bundle::Extraction {
            method: "manual_curation".to_string(),
            model: None,
            model_version: None,
            extracted_at: chrono::Utc::now().to_rfc3339(),
            extractor_version: env!("CARGO_PKG_VERSION").to_string(),
        },
        review: None,
        citation_count: None,
    };

    let mut dataset = crate::bundle::Dataset::new(
        name.to_string(),
        version.map(|s| s.to_string()),
        content_hash.to_string(),
        url.map(|s| s.to_string()),
        license.map(|s| s.to_string()),
        provenance,
    );
    dataset.row_count = row_count;

    if project.datasets.iter().any(|d| d.id == dataset.id) {
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "ok": false,
                    "command": "dataset.add",
                    "reason": "dataset_already_exists",
                    "id": dataset.id,
                }))
                .expect("serialize")
            );
        } else {
            println!(
                "{} dataset {} already exists in {}; skipping.",
                style::warn("dataset"),
                dataset.id,
                frontier.display()
            );
        }
        return;
    }

    let new_id = dataset.id.clone();
    project.datasets.push(dataset);
    repo::save_to_path(frontier, &project).unwrap_or_else(|e| fail_return(&e));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "dataset.add",
                "id": new_id,
                "name": name,
                "version": version,
                "frontier": frontier.display().to_string(),
            }))
            .expect("failed to serialize dataset.add result")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · DATASET · {}", new_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  name:          {name}");
        if let Some(v) = version {
            println!("  version:       {v}");
        }
        println!("  content_hash:  {content_hash}");
        if let Some(u) = url {
            println!("  url:           {u}");
        }
        println!("  source:        {source_title}");
        println!();
        println!(
            "  {} dataset recorded in {}",
            style::ok("ok"),
            frontier.display()
        );
    }
}

/// v0.49: deposit a NegativeResult through `state::add_negative_result`.
/// Builds the kind-specific payload, validates the variant fields up
/// front (so a missing `--power` for a registered_trial deposit fails
/// at the CLI boundary rather than deep in the validator), and prints
/// either a stable JSON envelope or a formatted summary.
#[allow(clippy::too_many_arguments)]
fn cmd_negative_result_add(
    frontier: &Path,
    kind: &str,
    deposited_by: &str,
    reason: &str,
    conditions_text: &str,
    notes: &str,
    targets: Vec<String>,
    endpoint: Option<&str>,
    intervention: Option<&str>,
    comparator: Option<&str>,
    population: Option<&str>,
    n_enrolled: Option<u32>,
    power: Option<f64>,
    ci_lower: Option<f64>,
    ci_upper: Option<f64>,
    effect_size_threshold: Option<f64>,
    registry_id: Option<&str>,
    reagent: Option<&str>,
    observation: Option<&str>,
    attempts: Option<u32>,
    source_title: &str,
    doi: Option<&str>,
    url: Option<&str>,
    year: Option<i32>,
    json: bool,
) {
    let nr_kind = match kind {
        "registered_trial" => {
            let endpoint =
                endpoint.unwrap_or_else(|| fail_return("--endpoint required for registered_trial"));
            let intervention = intervention
                .unwrap_or_else(|| fail_return("--intervention required for registered_trial"));
            let comparator = comparator
                .unwrap_or_else(|| fail_return("--comparator required for registered_trial"));
            let population = population
                .unwrap_or_else(|| fail_return("--population required for registered_trial"));
            let n_enrolled = n_enrolled
                .unwrap_or_else(|| fail_return("--n-enrolled required for registered_trial"));
            let power =
                power.unwrap_or_else(|| fail_return("--power required for registered_trial"));
            let ci_lower =
                ci_lower.unwrap_or_else(|| fail_return("--ci-lower required for registered_trial"));
            let ci_upper =
                ci_upper.unwrap_or_else(|| fail_return("--ci-upper required for registered_trial"));
            crate::bundle::NegativeResultKind::RegisteredTrial {
                endpoint: endpoint.to_string(),
                intervention: intervention.to_string(),
                comparator: comparator.to_string(),
                population: population.to_string(),
                n_enrolled,
                power,
                effect_size_ci: (ci_lower, ci_upper),
                effect_size_threshold,
                registry_id: registry_id.map(|s| s.to_string()),
            }
        }
        "exploratory" => {
            let reagent =
                reagent.unwrap_or_else(|| fail_return("--reagent required for exploratory"));
            let observation = observation
                .unwrap_or_else(|| fail_return("--observation required for exploratory"));
            let attempts =
                attempts.unwrap_or_else(|| fail_return("--attempts required for exploratory"));
            crate::bundle::NegativeResultKind::Exploratory {
                reagent: reagent.to_string(),
                observation: observation.to_string(),
                attempts,
            }
        }
        other => fail_return(&format!(
            "--kind must be 'registered_trial' or 'exploratory', got '{other}'"
        )),
    };

    let conditions = crate::bundle::Conditions {
        text: conditions_text.to_string(),
        species_verified: Vec::new(),
        species_unverified: Vec::new(),
        in_vitro: false,
        in_vivo: false,
        human_data: false,
        clinical_trial: matches!(kind, "registered_trial"),
        concentration_range: None,
        duration: None,
        age_group: None,
        cell_type: None,
    };

    let provenance = crate::bundle::Provenance {
        source_type: if matches!(kind, "registered_trial") {
            "clinical_trial".to_string()
        } else {
            "lab_notebook".to_string()
        },
        doi: doi.map(|s| s.to_string()),
        pmid: None,
        pmc: None,
        openalex_id: None,
        url: url.map(|s| s.to_string()),
        title: source_title.to_string(),
        authors: Vec::new(),
        year,
        journal: None,
        license: None,
        publisher: None,
        funders: Vec::new(),
        extraction: crate::bundle::Extraction {
            method: "manual_curation".to_string(),
            model: None,
            model_version: None,
            extracted_at: chrono::Utc::now().to_rfc3339(),
            extractor_version: env!("CARGO_PKG_VERSION").to_string(),
        },
        review: None,
        citation_count: None,
    };

    let report = state::add_negative_result(
        frontier,
        nr_kind,
        targets,
        deposited_by,
        conditions,
        provenance,
        notes,
        reason,
    )
    .unwrap_or_else(|e| fail_return(&e));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("serialize report")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · NEGATIVE-RESULT · {}", report.finding_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  kind:           {kind}");
        println!("  deposited_by:   {deposited_by}");
        if let Some(ev) = &report.applied_event_id {
            println!("  event:          {ev}");
        }
        println!(
            "  {} negative_result deposited in {}",
            style::ok("ok"),
            frontier.display()
        );
    }
}

/// v0.49: list NegativeResults in a frontier, optionally filtered by
/// the `vf_*` finding they bear against.
fn cmd_negative_results(frontier: &Path, target: Option<&str>, json: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let filtered: Vec<&crate::bundle::NegativeResult> = project
        .negative_results
        .iter()
        .filter(|nr| {
            target
                .map(|t| nr.target_findings.iter().any(|f| f == t))
                .unwrap_or(true)
        })
        .collect();

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "negative_results",
                "frontier": frontier.display().to_string(),
                "count": filtered.len(),
                "negative_results": filtered,
            }))
            .expect("serialize negative_results")
        );
        return;
    }

    if filtered.is_empty() {
        println!("  no negative_results in {}", frontier.display());
        return;
    }

    println!();
    println!(
        "  {} ({})",
        "VELA · NEGATIVE RESULTS".dimmed(),
        filtered.len()
    );
    println!("  {}", style::tick_row(60));
    for nr in &filtered {
        let kind_label = match &nr.kind {
            crate::bundle::NegativeResultKind::RegisteredTrial {
                endpoint, power, ..
            } => format!("trial · {endpoint} · power {power:.2}"),
            crate::bundle::NegativeResultKind::Exploratory {
                reagent, attempts, ..
            } => format!("exploratory · {reagent} · {attempts} attempts"),
        };
        let retracted = if nr.retracted { " [retracted]" } else { "" };
        let review = nr
            .review_state
            .as_ref()
            .map(|s| format!(" [{s:?}]"))
            .unwrap_or_default();
        println!("  {}{}{}", nr.id, retracted, review);
        println!("    {kind_label}");
        if !nr.target_findings.is_empty() {
            println!("    targets: {}", nr.target_findings.join(", "));
        }
    }
    println!();
}

/// v0.51: re-classify a kernel object's read-side access tier.
#[allow(clippy::too_many_arguments)]
fn cmd_tier_set(
    frontier: &Path,
    object_type: &str,
    object_id: &str,
    tier: &str,
    actor: &str,
    reason: &str,
    json: bool,
) {
    let parsed_tier =
        crate::access_tier::AccessTier::parse(tier).unwrap_or_else(|e| fail_return(&e));
    let report = state::set_tier(frontier, object_type, object_id, parsed_tier, actor, reason)
        .unwrap_or_else(|e| fail_return(&e));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("serialize tier-set report")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · TIER · {}", object_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  object_type:    {object_type}");
        println!("  new_tier:       {}", parsed_tier.canonical());
        println!("  actor:          {actor}");
        if let Some(ev) = &report.applied_event_id {
            println!("  event:          {ev}");
        }
        println!("  {} tier set in {}", style::ok("ok"), frontier.display());
    }
}

/// v0.50: open a Trajectory.
#[allow(clippy::too_many_arguments)]
fn cmd_trajectory_create(
    frontier: &Path,
    deposited_by: &str,
    reason: &str,
    targets: Vec<String>,
    notes: &str,
    json: bool,
) {
    let report = state::create_trajectory(frontier, targets, deposited_by, notes, reason)
        .unwrap_or_else(|e| fail_return(&e));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("serialize trajectory report")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · TRAJECTORY · {}", report.finding_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  deposited_by:   {deposited_by}");
        if let Some(ev) = &report.applied_event_id {
            println!("  event:          {ev}");
        }
        println!(
            "  {} trajectory opened in {}",
            style::ok("ok"),
            frontier.display()
        );
    }
}

/// v0.50: append a step to a Trajectory.
#[allow(clippy::too_many_arguments)]
fn cmd_trajectory_step(
    frontier: &Path,
    trajectory_id: &str,
    kind: &str,
    description: &str,
    actor: &str,
    reason: &str,
    references: Vec<String>,
    json: bool,
) {
    let parsed_kind = match kind {
        "hypothesis" => crate::bundle::TrajectoryStepKind::Hypothesis,
        "tried" => crate::bundle::TrajectoryStepKind::Tried,
        "ruled_out" => crate::bundle::TrajectoryStepKind::RuledOut,
        "observed" => crate::bundle::TrajectoryStepKind::Observed,
        "refined" => crate::bundle::TrajectoryStepKind::Refined,
        other => fail_return(&format!(
            "--kind must be one of hypothesis|tried|ruled_out|observed|refined, got '{other}'"
        )),
    };
    let report = state::append_trajectory_step(
        frontier,
        trajectory_id,
        parsed_kind,
        description,
        actor,
        references,
        reason,
    )
    .unwrap_or_else(|e| fail_return(&e));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("serialize step report")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · STEP · {}", report.finding_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  trajectory:     {trajectory_id}");
        println!("  kind:           {kind}");
        println!("  actor:          {actor}");
        println!(
            "  {} step appended in {}",
            style::ok("ok"),
            frontier.display()
        );
    }
}

/// v0.50: list Trajectories in a frontier.
fn cmd_trajectories(frontier: &Path, target: Option<&str>, json: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let filtered: Vec<&crate::bundle::Trajectory> = project
        .trajectories
        .iter()
        .filter(|t| {
            target
                .map(|tg| t.target_findings.iter().any(|f| f == tg))
                .unwrap_or(true)
        })
        .collect();

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "trajectories",
                "frontier": frontier.display().to_string(),
                "count": filtered.len(),
                "trajectories": filtered,
            }))
            .expect("serialize trajectories")
        );
        return;
    }

    if filtered.is_empty() {
        println!("  no trajectories in {}", frontier.display());
        return;
    }

    println!();
    println!("  {} ({})", "VELA · TRAJECTORIES".dimmed(), filtered.len());
    println!("  {}", style::tick_row(60));
    for t in &filtered {
        let retracted = if t.retracted { " [retracted]" } else { "" };
        let review = t
            .review_state
            .as_ref()
            .map(|s| format!(" [{s:?}]"))
            .unwrap_or_default();
        println!("  {}{}{}", t.id, retracted, review);
        println!(
            "    {} step(s){}",
            t.steps.len(),
            if t.target_findings.is_empty() {
                String::new()
            } else {
                format!(" · targets: {}", t.target_findings.join(", "))
            }
        );
        for step in &t.steps {
            let label = match step.kind {
                crate::bundle::TrajectoryStepKind::Hypothesis => "hypothesis",
                crate::bundle::TrajectoryStepKind::Tried => "tried",
                crate::bundle::TrajectoryStepKind::RuledOut => "ruled_out",
                crate::bundle::TrajectoryStepKind::Observed => "observed",
                crate::bundle::TrajectoryStepKind::Refined => "refined",
            };
            let preview: String = step.description.chars().take(80).collect();
            println!("      [{label}] {preview}");
        }
    }
    println!();
}

/// v0.33: list datasets in a frontier.
fn cmd_datasets(frontier: &Path, json: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "datasets",
                "frontier": frontier.display().to_string(),
                "count": project.datasets.len(),
                "datasets": project.datasets,
            }))
            .expect("serialize datasets")
        );
        return;
    }
    println!();
    println!(
        "  {}",
        format!("VELA · DATASETS · {}", frontier.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if project.datasets.is_empty() {
        println!("  (no datasets registered)");
        return;
    }
    for ds in &project.datasets {
        let v = ds
            .version
            .as_deref()
            .map(|s| format!("@{s}"))
            .unwrap_or_default();
        println!("  · {}  {}{}", ds.id.dimmed(), ds.name, v);
        if let Some(u) = &ds.url {
            println!("      url:    {}", truncate(u, 80));
        }
        println!("      hash:   {}", truncate(&ds.content_hash, 80));
    }
}

/// v0.33: append a CodeArtifact record to a frontier and persist it.
#[allow(clippy::too_many_arguments)]
fn cmd_code_add(
    frontier: &Path,
    language: &str,
    repo_url: Option<&str>,
    commit: Option<&str>,
    path: &str,
    content_hash: &str,
    line_start: Option<u32>,
    line_end: Option<u32>,
    entry_point: Option<&str>,
    json: bool,
) {
    let mut project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));

    let line_range = match (line_start, line_end) {
        (Some(a), Some(b)) => Some((a, b)),
        (Some(a), None) => Some((a, a)),
        _ => None,
    };

    let artifact = crate::bundle::CodeArtifact::new(
        language.to_string(),
        repo_url.map(|s| s.to_string()),
        commit.map(|s| s.to_string()),
        path.to_string(),
        line_range,
        content_hash.to_string(),
        entry_point.map(|s| s.to_string()),
    );

    if project.code_artifacts.iter().any(|c| c.id == artifact.id) {
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "ok": false,
                    "command": "code.add",
                    "reason": "artifact_already_exists",
                    "id": artifact.id,
                }))
                .expect("serialize")
            );
        } else {
            println!(
                "{} code artifact {} already exists in {}; skipping.",
                style::warn("code"),
                artifact.id,
                frontier.display()
            );
        }
        return;
    }

    let new_id = artifact.id.clone();
    project.code_artifacts.push(artifact);
    repo::save_to_path(frontier, &project).unwrap_or_else(|e| fail_return(&e));

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "code.add",
                "id": new_id,
                "language": language,
                "path": path,
                "frontier": frontier.display().to_string(),
            }))
            .expect("failed to serialize code.add result")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · CODE · {}", new_id).to_uppercase().dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  language:      {language}");
        if let Some(r) = repo_url {
            println!("  repo:          {r}");
        }
        if let Some(c) = commit {
            println!("  commit:        {c}");
        }
        println!("  path:          {path}");
        if let Some((a, b)) = line_range {
            println!("  lines:         {a}-{b}");
        }
        println!("  content_hash:  {content_hash}");
        println!();
        println!(
            "  {} code artifact recorded in {}",
            style::ok("ok"),
            frontier.display()
        );
    }
}

/// v0.33: list code artifacts in a frontier.
fn cmd_code_artifacts(frontier: &Path, json: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "code-artifacts",
                "frontier": frontier.display().to_string(),
                "count": project.code_artifacts.len(),
                "code_artifacts": project.code_artifacts,
            }))
            .expect("serialize code-artifacts")
        );
        return;
    }
    println!();
    println!(
        "  {}",
        format!("VELA · CODE · {}", frontier.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if project.code_artifacts.is_empty() {
        println!("  (no code artifacts registered)");
        return;
    }
    for c in &project.code_artifacts {
        let lr = c
            .line_range
            .map(|(a, b)| format!(":{a}-{b}"))
            .unwrap_or_default();
        println!("  · {}  {} {}{}", c.id.dimmed(), c.language, c.path, lr);
        if let Some(r) = &c.repo_url {
            println!("      repo:   {}", truncate(r, 80));
        }
        if let Some(g) = &c.git_commit {
            println!("      commit: {g}");
        }
    }
}

fn sha256_for_bytes(bytes: &[u8]) -> String {
    format!("sha256:{}", hex::encode(Sha256::digest(bytes)))
}

fn sha256_hex_part(content_hash: &str) -> &str {
    content_hash.strip_prefix("sha256:").unwrap_or(content_hash)
}

fn artifact_blob_locator(frontier: &Path, content_hash: &str, bytes: &[u8]) -> Option<String> {
    let Ok(repo::VelaSource::VelaRepo(root)) = repo::detect(frontier) else {
        return None;
    };
    let hex = sha256_hex_part(content_hash);
    let rel = format!(".vela/artifact-blobs/sha256/{hex}");
    let path = root.join(&rel);
    if let Some(parent) = path.parent() {
        std::fs::create_dir_all(parent).unwrap_or_else(|e| {
            fail(&format!(
                "Failed to create artifact blob directory {}: {e}",
                parent.display()
            ))
        });
    }
    if !path.is_file() {
        std::fs::write(&path, bytes)
            .unwrap_or_else(|e| fail(&format!("Failed to write artifact blob: {e}")));
    }
    Some(rel)
}

fn parse_metadata_pairs(pairs: Vec<String>) -> BTreeMap<String, Value> {
    let mut out = BTreeMap::new();
    for pair in pairs {
        let Some((key, value)) = pair.split_once('=') else {
            fail(&format!("--metadata must be key=value, got {pair:?}"));
        };
        let key = key.trim();
        if key.is_empty() {
            fail("--metadata key must be non-empty");
        }
        out.insert(key.to_string(), Value::String(value.trim().to_string()));
    }
    out
}

fn artifact_source_type(kind: &str) -> &'static str {
    match kind {
        "clinical_trial_record" | "protocol" => "clinical_trial",
        "dataset" => "data_release",
        "model_output" => "model_output",
        "registry_record" => "database_record",
        "lab_file" => "lab_notebook",
        _ => "database_record",
    }
}

fn artifact_provenance(
    kind: &str,
    title: &str,
    url: Option<&str>,
    doi: Option<&str>,
    license: Option<&str>,
) -> crate::bundle::Provenance {
    crate::bundle::Provenance {
        source_type: artifact_source_type(kind).to_string(),
        doi: doi.map(str::to_string),
        pmid: None,
        pmc: None,
        openalex_id: None,
        url: url.map(str::to_string),
        title: title.to_string(),
        authors: Vec::new(),
        year: None,
        journal: None,
        license: license.map(str::to_string),
        publisher: None,
        funders: Vec::new(),
        extraction: crate::bundle::Extraction {
            method: "artifact_deposit".to_string(),
            model: None,
            model_version: None,
            extracted_at: chrono::Utc::now().to_rfc3339(),
            extractor_version: env!("CARGO_PKG_VERSION").to_string(),
        },
        review: None,
        citation_count: None,
    }
}

#[allow(clippy::too_many_arguments)]
fn cmd_artifact_add(
    frontier: &Path,
    kind: &str,
    name: &str,
    file: Option<&Path>,
    url: Option<&str>,
    content_hash: Option<&str>,
    media_type: Option<&str>,
    license: Option<&str>,
    source_title: Option<&str>,
    source_url: Option<&str>,
    doi: Option<&str>,
    target: Vec<String>,
    metadata: Vec<String>,
    access_tier: &str,
    deposited_by: &str,
    reason: &str,
    json_out: bool,
) {
    let tier =
        crate::access_tier::AccessTier::parse(access_tier).unwrap_or_else(|e| fail_return(&e));
    let mut size_bytes = None;
    let mut storage_mode = "pointer".to_string();
    let mut locator = url.map(str::to_string);
    let mut computed_hash = content_hash.map(str::to_string);

    if let Some(path) = file {
        let bytes = std::fs::read(path)
            .unwrap_or_else(|e| fail(&format!("Failed to read artifact file: {e}")));
        let actual_hash = sha256_for_bytes(&bytes);
        if let Some(expected) = content_hash {
            let expected_hex = sha256_hex_part(expected);
            let actual_hex = sha256_hex_part(&actual_hash);
            if !expected_hex.eq_ignore_ascii_case(actual_hex) {
                fail(&format!(
                    "--content-hash does not match file bytes: expected {expected}, got {actual_hash}"
                ));
            }
        }
        size_bytes = Some(bytes.len() as u64);
        computed_hash = Some(actual_hash.clone());
        if let Some(rel) = artifact_blob_locator(frontier, &actual_hash, &bytes) {
            storage_mode = "local_blob".to_string();
            locator = Some(rel);
        } else {
            storage_mode = "local_file".to_string();
            locator = Some(path.display().to_string());
        }
    }

    let Some(content_hash) = computed_hash else {
        fail("Provide --content-hash unless --file is present.");
    };
    let content_hash_for_print = content_hash.clone();
    if file.is_none() && url.is_some() {
        storage_mode = "remote".to_string();
    }

    let source_url_effective = source_url.or(url);
    let source_title = source_title.unwrap_or(name);
    let provenance = artifact_provenance(kind, source_title, source_url_effective, doi, license);
    let metadata = parse_metadata_pairs(metadata);
    let artifact = crate::bundle::Artifact::new(
        kind.to_string(),
        name.to_string(),
        content_hash,
        size_bytes,
        media_type.map(str::to_string),
        storage_mode,
        locator,
        source_url_effective.map(str::to_string),
        license.map(str::to_string),
        target,
        provenance,
        metadata,
        tier,
    )
    .unwrap_or_else(|e| fail_return(&e));

    let artifact_id = artifact.id.clone();
    let report = state::add_artifact(frontier, artifact, deposited_by, reason)
        .unwrap_or_else(|e| fail_return(&e));

    if json_out {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "artifact.add",
                "id": artifact_id,
                "frontier": frontier.display().to_string(),
                "event": report.applied_event_id,
            }))
            .expect("serialize artifact.add")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · ARTIFACT · {}", artifact_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  kind:          {kind}");
        println!("  name:          {name}");
        println!("  hash:          {content_hash_for_print}");
        println!(
            "  {} artifact recorded in {}",
            style::ok("ok"),
            frontier.display()
        );
    }
}

fn cmd_artifacts(frontier: &Path, target: Option<&str>, json_out: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let filtered: Vec<&crate::bundle::Artifact> = project
        .artifacts
        .iter()
        .filter(|artifact| {
            target
                .map(|t| artifact.target_findings.iter().any(|f| f == t))
                .unwrap_or(true)
        })
        .collect();

    if json_out {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "artifacts",
                "frontier": frontier.display().to_string(),
                "count": filtered.len(),
                "artifacts": filtered,
            }))
            .expect("serialize artifacts")
        );
        return;
    }

    println!();
    println!(
        "  {}",
        format!("VELA · ARTIFACTS · {}", frontier.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if filtered.is_empty() {
        println!("  (no artifacts registered)");
        return;
    }
    for artifact in filtered {
        println!(
            "  · {}  {} · {}",
            artifact.id.dimmed(),
            artifact.kind,
            artifact.name
        );
        if let Some(locator) = &artifact.locator {
            println!("      locator: {}", truncate(locator, 88));
        }
        if !artifact.target_findings.is_empty() {
            println!("      targets: {}", artifact.target_findings.join(", "));
        }
    }
}

fn cmd_artifact_audit(frontier: &Path, json_out: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let audit = crate::artifact_audit::audit_artifacts(frontier, &project);
    if json_out {
        println!(
            "{}",
            serde_json::to_string_pretty(&audit).expect("serialize artifact audit")
        );
        if !audit.ok {
            std::process::exit(1);
        }
        return;
    }

    println!();
    println!(
        "  {}",
        format!("VELA · ARTIFACT AUDIT · {}", frontier.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    println!("  artifacts: {}", audit.artifact_count);
    println!("  checked local blobs: {}", audit.checked_local_blobs);
    println!("  local blob bytes: {}", audit.local_blob_bytes);
    if !audit.by_kind.is_empty() {
        let kinds = audit
            .by_kind
            .iter()
            .map(|(kind, count)| format!("{kind}:{count}"))
            .collect::<Vec<_>>()
            .join(", ");
        println!("  kinds: {kinds}");
    }
    if audit.ok {
        println!("  {} artifact audit passed.", style::ok("ok"));
        return;
    }
    for issue in &audit.issues {
        println!(
            "  {} {} {}: {}",
            style::lost("invalid"),
            issue.id,
            issue.field,
            issue.message
        );
    }
    std::process::exit(1);
}

fn cmd_decision_brief(frontier: &Path, json_out: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let report = decision::load_decision_brief(frontier, &project);
    if json_out {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("serialize decision brief report")
        );
        if !report.ok {
            std::process::exit(1);
        }
        return;
    }
    println!();
    println!(
        "  {}",
        format!("VELA · DECISION BRIEF · {}", project.project.name)
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if !report.ok {
        print_projection_issues(&report.issues, report.error.as_deref());
        std::process::exit(1);
    }
    let brief = report
        .projection
        .as_ref()
        .expect("ok decision report carries projection");
    for question in &brief.questions {
        println!("  · {} · {}", question.id.dimmed(), question.title);
        println!("      answer: {}", wrap_line(&question.short_answer, 82));
        println!("      caveat: {}", wrap_line(&question.caveat, 82));
        println!("      support: {}", question.supporting_findings.join(", "));
        if !question.tension_findings.is_empty() {
            println!("      tensions: {}", question.tension_findings.join(", "));
        }
        if !question.gap_findings.is_empty() {
            println!("      gaps: {}", question.gap_findings.join(", "));
        }
        if !question.artifact_ids.is_empty() {
            println!("      artifacts: {}", question.artifact_ids.join(", "));
        }
        println!(
            "      would change: {}",
            wrap_line(&question.what_would_change_this_answer, 82)
        );
    }
}

fn cmd_trial_summary(frontier: &Path, json_out: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let report = decision::load_trial_outcomes(frontier, &project);
    if json_out {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("serialize trial summary report")
        );
        if !report.ok {
            std::process::exit(1);
        }
        return;
    }
    println!();
    println!(
        "  {}",
        format!("VELA · TRIAL SUMMARY · {}", project.project.name)
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if !report.ok {
        print_projection_issues(&report.issues, report.error.as_deref());
        std::process::exit(1);
    }
    let outcomes = report
        .projection
        .as_ref()
        .expect("ok trial report carries projection");
    for row in &outcomes.rows {
        println!("  · {} · {} ({})", row.id.dimmed(), row.program, row.drug);
        println!("      population: {}", wrap_line(&row.population, 82));
        println!("      endpoint: {}", wrap_line(&row.primary_endpoint, 82));
        println!("      cognition: {}", wrap_line(&row.cognitive_result, 82));
        println!("      biomarker: {}", wrap_line(&row.biomarker_result, 82));
        println!("      risk: {}", wrap_line(&row.aria_or_safety_result, 82));
        println!("      status: {}", wrap_line(&row.regulatory_status, 82));
        if !row.finding_ids.is_empty() {
            println!("      findings: {}", row.finding_ids.join(", "));
        }
        if !row.artifact_ids.is_empty() {
            println!("      artifacts: {}", row.artifact_ids.join(", "));
        }
    }
}

fn cmd_source_verification(frontier: &Path, json_out: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let report = decision::load_source_verification(frontier, &project);
    if json_out {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("serialize source verification report")
        );
        if !report.ok {
            std::process::exit(1);
        }
        return;
    }
    println!();
    println!(
        "  {}",
        format!("VELA · SOURCE VERIFICATION · {}", project.project.name)
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if !report.ok {
        print_projection_issues(&report.issues, report.error.as_deref());
        std::process::exit(1);
    }
    let verification = report
        .projection
        .as_ref()
        .expect("ok source verification report carries projection");
    println!("  verified_at: {}", verification.verified_at);
    for source in &verification.sources {
        println!("  · {} · {}", source.id.dimmed(), source.title);
        println!("      agency: {}", source.agency);
        println!("      url: {}", truncate(&source.url, 88));
        println!("      status: {}", wrap_line(&source.current_status, 82));
    }
}

fn cmd_source_ingest_plan(frontier: &Path, json_out: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let report = decision::load_source_ingest_plan(frontier, &project);
    if json_out {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("serialize source ingest plan report")
        );
        if !report.ok {
            std::process::exit(1);
        }
        return;
    }
    println!();
    println!(
        "  {}",
        format!("VELA · SOURCE INGEST PLAN · {}", project.project.name)
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if !report.ok {
        print_projection_issues(&report.issues, report.error.as_deref());
        std::process::exit(1);
    }
    let plan = report
        .projection
        .as_ref()
        .expect("ok source ingest plan report carries projection");
    println!("  verified_at: {}", plan.verified_at);
    println!("  entries: {}", plan.entries.len());
    for entry in &plan.entries {
        println!(
            "  · {} · {} · {} · {}",
            entry.id.dimmed(),
            entry.category,
            entry.priority,
            entry.ingest_status
        );
        println!("      name: {}", wrap_line(&entry.name, 82));
        println!("      locator: {}", truncate(&entry.locator, 88));
        println!("      use: {}", wrap_line(&entry.target_use, 82));
        if let Some(id) = &entry.current_frontier_artifact_id {
            println!("      artifact: {id}");
        }
        if !entry.target_findings.is_empty() {
            println!("      findings: {}", entry.target_findings.join(", "));
        }
    }
}

fn print_projection_issues(issues: &[decision::ProjectionIssue], error: Option<&str>) {
    if let Some(error) = error {
        println!("  {} {error}", style::lost("unavailable"));
    }
    for issue in issues {
        println!(
            "  {} {}: {}",
            style::lost("invalid"),
            issue.path,
            issue.message
        );
    }
}

fn wrap_line(text: &str, max_chars: usize) -> String {
    if text.chars().count() <= max_chars {
        return text.to_string();
    }
    let mut out = String::new();
    let mut line_len = 0usize;
    for word in text.split_whitespace() {
        let word_len = word.chars().count();
        if line_len > 0 && line_len + 1 + word_len > max_chars {
            out.push('\n');
            out.push_str("              ");
            out.push_str(word);
            line_len = word_len;
        } else {
            if line_len > 0 {
                out.push(' ');
                line_len += 1;
            }
            out.push_str(word);
            line_len += word_len;
        }
    }
    out
}

fn clinical_str<'a>(study: &'a Value, pointer: &str) -> Option<&'a str> {
    study.pointer(pointer).and_then(Value::as_str)
}

fn clinical_string_array(study: &Value, pointer: &str) -> Vec<String> {
    study
        .pointer(pointer)
        .and_then(Value::as_array)
        .map(|items| {
            items
                .iter()
                .filter_map(Value::as_str)
                .map(str::to_string)
                .collect()
        })
        .unwrap_or_default()
}

fn clinical_named_array(study: &Value, pointer: &str, field: &str) -> Vec<String> {
    study
        .pointer(pointer)
        .and_then(Value::as_array)
        .map(|items| {
            items
                .iter()
                .filter_map(|item| item.get(field).and_then(Value::as_str))
                .map(str::to_string)
                .collect()
        })
        .unwrap_or_default()
}

fn insert_string_vec_metadata(
    metadata: &mut BTreeMap<String, Value>,
    key: &str,
    values: Vec<String>,
) {
    if values.is_empty() {
        return;
    }
    metadata.insert(
        key.to_string(),
        Value::Array(values.into_iter().map(Value::String).collect()),
    );
}

async fn cmd_clinical_trial_import(
    frontier: &Path,
    nct_id: &str,
    input_json: Option<&Path>,
    target: Vec<String>,
    deposited_by: &str,
    reason: &str,
    license: &str,
    json_out: bool,
) {
    let api_url = format!("https://clinicaltrials.gov/api/v2/studies/{nct_id}");
    let raw = if let Some(path) = input_json {
        std::fs::read_to_string(path)
            .unwrap_or_else(|e| fail(&format!("Failed to read ClinicalTrials.gov JSON: {e}")))
    } else {
        let response = reqwest::get(&api_url).await.unwrap_or_else(|e| {
            fail(&format!(
                "Failed to fetch ClinicalTrials.gov record {nct_id}: {e}"
            ))
        });
        let response = response.error_for_status().unwrap_or_else(|e| {
            fail(&format!(
                "Failed to fetch ClinicalTrials.gov record {nct_id}: {e}"
            ))
        });
        response.text().await.unwrap_or_else(|e| {
            fail(&format!(
                "Failed to read ClinicalTrials.gov record {nct_id}: {e}"
            ))
        })
    };
    let study: Value = serde_json::from_str(&raw)
        .unwrap_or_else(|e| fail(&format!("Failed to parse ClinicalTrials.gov JSON: {e}")));
    let canonical_bytes = crate::canonical::to_canonical_bytes(&study)
        .unwrap_or_else(|e| fail(&format!("Failed to canonicalize trial JSON: {e}")));
    let content_hash = sha256_for_bytes(&canonical_bytes);
    let locator = artifact_blob_locator(frontier, &content_hash, &canonical_bytes)
        .unwrap_or_else(|| api_url.clone());
    let storage_mode = if locator.starts_with(".vela/") {
        "local_blob"
    } else {
        "remote"
    };

    let parsed_nct = clinical_str(&study, "/protocolSection/identificationModule/nctId")
        .unwrap_or(nct_id)
        .to_string();
    let title = clinical_str(&study, "/protocolSection/identificationModule/briefTitle")
        .or_else(|| {
            clinical_str(
                &study,
                "/protocolSection/identificationModule/officialTitle",
            )
        })
        .unwrap_or(nct_id);
    let public_url = format!("https://clinicaltrials.gov/study/{parsed_nct}");
    let mut metadata = BTreeMap::new();
    metadata.insert("nct_id".to_string(), Value::String(parsed_nct.clone()));
    metadata.insert(
        "source_api".to_string(),
        Value::String("clinicaltrials.gov-v2".to_string()),
    );
    metadata.insert(
        "retrieved_at".to_string(),
        Value::String(chrono::Utc::now().to_rfc3339()),
    );
    for (key, pointer) in [
        (
            "overall_status",
            "/protocolSection/statusModule/overallStatus",
        ),
        (
            "start_date",
            "/protocolSection/statusModule/startDateStruct/date",
        ),
        (
            "completion_date",
            "/protocolSection/statusModule/completionDateStruct/date",
        ),
    ] {
        if let Some(value) = clinical_str(&study, pointer) {
            metadata.insert(key.to_string(), Value::String(value.to_string()));
        }
    }
    insert_string_vec_metadata(
        &mut metadata,
        "phases",
        clinical_string_array(&study, "/protocolSection/designModule/phases"),
    );
    insert_string_vec_metadata(
        &mut metadata,
        "conditions",
        clinical_string_array(&study, "/protocolSection/conditionsModule/conditions"),
    );
    insert_string_vec_metadata(
        &mut metadata,
        "interventions",
        clinical_named_array(
            &study,
            "/protocolSection/armsInterventionsModule/interventions",
            "name",
        ),
    );
    insert_string_vec_metadata(
        &mut metadata,
        "primary_outcomes",
        clinical_named_array(
            &study,
            "/protocolSection/outcomesModule/primaryOutcomes",
            "measure",
        ),
    );
    if let Some(has_results) = study.get("hasResults").and_then(Value::as_bool) {
        metadata.insert("has_results".to_string(), Value::Bool(has_results));
    }

    let provenance = artifact_provenance(
        "clinical_trial_record",
        title,
        Some(&public_url),
        None,
        Some(license),
    );
    let artifact = crate::bundle::Artifact::new(
        "clinical_trial_record",
        title.to_string(),
        content_hash,
        Some(canonical_bytes.len() as u64),
        Some("application/json".to_string()),
        storage_mode.to_string(),
        Some(locator),
        Some(public_url.clone()),
        Some(license.to_string()),
        target,
        provenance,
        metadata,
        crate::access_tier::AccessTier::Public,
    )
    .unwrap_or_else(|e| fail_return(&e));
    let artifact_id = artifact.id.clone();
    let report = state::add_artifact(frontier, artifact, deposited_by, reason)
        .unwrap_or_else(|e| fail_return(&e));

    if json_out {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "clinical-trial-import",
                "nct_id": parsed_nct,
                "id": artifact_id,
                "frontier": frontier.display().to_string(),
                "event": report.applied_event_id,
                "source_url": public_url,
            }))
            .expect("serialize clinical-trial-import")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · CLINICAL TRIAL · {}", artifact_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  nct_id:        {parsed_nct}");
        println!("  title:         {}", truncate(title, 96));
        println!("  source:        {public_url}");
        println!(
            "  {} trial record imported into {}",
            style::ok("ok"),
            frontier.display()
        );
    }
}

/// v0.32: append a Replication attempt to a frontier.
///
/// Validates the outcome label, builds a `Replication` with a fresh
/// content-addressed id, persists it, and prints either a structured
/// JSON receipt or a human summary. Refuses to write if the target
/// finding is not present in the frontier.
#[allow(clippy::too_many_arguments)]
fn cmd_replicate(
    frontier: &Path,
    target: &str,
    outcome: &str,
    attempted_by: &str,
    conditions_text: &str,
    source_title: &str,
    doi: Option<&str>,
    pmid: Option<&str>,
    sample_size: Option<&str>,
    note: &str,
    previous_attempt: Option<&str>,
    no_cascade: bool,
    json: bool,
) {
    if !crate::bundle::VALID_REPLICATION_OUTCOMES.contains(&outcome) {
        fail(&format!(
            "invalid outcome '{outcome}'; valid: {:?}",
            crate::bundle::VALID_REPLICATION_OUTCOMES
        ));
    }
    if !target.starts_with("vf_") {
        fail(&format!("target '{target}' is not a vf_ finding id"));
    }

    let mut project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));

    if !project.findings.iter().any(|f| f.id == target) {
        fail(&format!(
            "target finding '{target}' not present in frontier '{}'",
            frontier.display()
        ));
    }

    // Build the conditions, evidence, provenance for the replication.
    // Conditions text is what enters the content-address preimage; we
    // also lift in_vivo/in_vitro/human_data flags from common keywords
    // so confidence math behaves sensibly downstream.
    let lower = conditions_text.to_lowercase();
    let conditions = crate::bundle::Conditions {
        text: conditions_text.to_string(),
        species_verified: Vec::new(),
        species_unverified: Vec::new(),
        in_vitro: lower.contains("in vitro") || lower.contains("ipsc"),
        in_vivo: lower.contains("in vivo") || lower.contains("mouse") || lower.contains("rat"),
        human_data: lower.contains("human")
            || lower.contains("clinical")
            || lower.contains("patient"),
        clinical_trial: lower.contains("clinical trial") || lower.contains("phase "),
        concentration_range: None,
        duration: None,
        age_group: None,
        cell_type: None,
    };

    let evidence = crate::bundle::Evidence {
        evidence_type: "experimental".to_string(),
        model_system: String::new(),
        species: None,
        method: "replication_attempt".to_string(),
        sample_size: sample_size.map(|s| s.to_string()),
        effect_size: None,
        p_value: None,
        replicated: outcome == "replicated",
        replication_count: None,
        evidence_spans: Vec::new(),
    };

    let provenance = crate::bundle::Provenance {
        source_type: "published_paper".to_string(),
        doi: doi.map(|s| s.to_string()),
        pmid: pmid.map(|s| s.to_string()),
        pmc: None,
        openalex_id: None,
        url: None,
        title: source_title.to_string(),
        authors: Vec::new(),
        year: None,
        journal: None,
        license: None,
        publisher: None,
        funders: Vec::new(),
        extraction: crate::bundle::Extraction {
            method: "manual_curation".to_string(),
            model: None,
            model_version: None,
            extracted_at: chrono::Utc::now().to_rfc3339(),
            extractor_version: env!("CARGO_PKG_VERSION").to_string(),
        },
        review: None,
        citation_count: None,
    };

    let mut rep = crate::bundle::Replication::new(
        target.to_string(),
        attempted_by.to_string(),
        outcome.to_string(),
        evidence,
        conditions,
        provenance,
        note.to_string(),
    );
    rep.previous_attempt = previous_attempt.map(|s| s.to_string());

    // Refuse to write if the same vrep_id already exists (idempotent
    // re-runs are safe; conflicts surface here).
    if project.replications.iter().any(|r| r.id == rep.id) {
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "ok": false,
                    "command": "replicate",
                    "reason": "replication_already_exists",
                    "id": rep.id,
                }))
                .expect("serialize")
            );
        } else {
            println!(
                "{} replication {} already exists in {}; skipping.",
                style::warn("replicate"),
                rep.id,
                frontier.display()
            );
        }
        return;
    }

    let new_id = rep.id.clone();
    project.replications.push(rep);

    // v0.36.2: trigger the replication-aware propagation cascade. The
    // target's confidence is recomputed from the now-updated
    // `project.replications` collection (closes the A.1 loop) and
    // dependents are flagged for review with `upstream_replication_*`.
    // `inconclusive` outcomes do not cascade; we still call propagate
    // so the source-side recompute always runs.
    let cascade_result = if no_cascade {
        None
    } else {
        let result = propagate::propagate_correction(
            &mut project,
            target,
            propagate::PropagationAction::ReplicationOutcome {
                outcome: outcome.to_string(),
                vrep_id: new_id.clone(),
            },
        );
        // Persist propagation events into the canonical review log.
        // Without this, the events are emitted to stdout and lost.
        project.review_events.extend(result.events.clone());
        project::recompute_stats(&mut project);
        Some(result)
    };

    repo::save_to_path(frontier, &project).unwrap_or_else(|e| fail_return(&e));

    if json {
        let cascade_json = cascade_result.as_ref().map(|r| {
            json!({
                "affected": r.affected,
                "events": r.events.len(),
            })
        });
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "replicate",
                "id": new_id,
                "target": target,
                "outcome": outcome,
                "attempted_by": attempted_by,
                "cascade": cascade_json,
                "frontier": frontier.display().to_string(),
            }))
            .expect("failed to serialize replicate result")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · REPLICATE · {}", new_id)
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  target:        {target}");
        println!("  outcome:       {outcome}");
        println!("  attempted by:  {attempted_by}");
        println!("  conditions:    {conditions_text}");
        println!("  source:        {source_title}");
        if let Some(d) = doi {
            println!("  doi:           {d}");
        }
        println!();
        println!(
            "  {} replication recorded in {}",
            style::ok("ok"),
            frontier.display()
        );
        if let Some(result) = cascade_result {
            println!(
                "  {} cascade: {} dependent(s) flagged, {} review event(s) recorded",
                style::ok("ok"),
                result.affected,
                result.events.len()
            );
        } else {
            println!("  {} cascade skipped (--no-cascade)", style::warn("info"));
        }
    }
}

/// v0.32: list replications in a frontier, optionally filtered by target.
fn cmd_replications(frontier: &Path, target: Option<&str>, json: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let filtered: Vec<&crate::bundle::Replication> = project
        .replications
        .iter()
        .filter(|r| target.is_none_or(|t| r.target_finding == t))
        .collect();

    if json {
        let payload = json!({
            "ok": true,
            "command": "replications",
            "frontier": frontier.display().to_string(),
            "filter_target": target,
            "count": filtered.len(),
            "replications": filtered,
        });
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize replications list")
        );
        return;
    }

    println!();
    let header = match target {
        Some(t) => format!("VELA · REPLICATIONS · {t}"),
        None => format!("VELA · REPLICATIONS · {}", frontier.display()),
    };
    println!("  {}", header.to_uppercase().dimmed());
    println!("  {}", style::tick_row(60));
    if filtered.is_empty() {
        println!("  (no replications recorded)");
        return;
    }
    for rep in &filtered {
        let outcome_chip = match rep.outcome.as_str() {
            "replicated" => style::ok(&rep.outcome),
            "failed" => style::lost(&rep.outcome),
            "partial" => style::warn(&rep.outcome),
            _ => rep.outcome.clone().normal().to_string(),
        };
        println!(
            "  · {}  {}  by {}",
            rep.id.dimmed(),
            outcome_chip,
            rep.attempted_by
        );
        println!("      target:     {}", rep.target_finding);
        if !rep.conditions.text.is_empty() {
            println!("      conditions: {}", truncate(&rep.conditions.text, 80));
        }
        if !rep.provenance.title.is_empty() {
            println!("      source:     {}", truncate(&rep.provenance.title, 80));
        }
    }
}

/// v0.74: file-extension dispatcher for `vela ingest`. Routes one
/// path or stable identifier URI to the right backing path.
///
/// - `doi:` / `pmid:` / `nct:` URI -> `cmd_source_fetch`.
/// - JSON file (Carina-shaped artifact packet) -> `cmd_artifact_to_state`.
/// - PDF file or folder of PDFs -> `cmd_scout`. Folder is the
///   supported shape today; single-file mode lands in v0.74.2.
/// - Markdown file or folder -> `cmd_compile_notes`.
/// - CSV / TSV file or folder -> `cmd_compile_data`.
/// - Other directory -> `cmd_compile_code`.
///
/// No new substrate logic; just routing under one verb.
async fn cmd_ingest(
    path: &str,
    frontier: &Path,
    backend: Option<&str>,
    actor: Option<&str>,
    dry_run: bool,
    json: bool,
) {
    // Stable identifier URI: dispatch to source-fetch.
    let lowered = path.trim().to_lowercase();
    if lowered.starts_with("doi:") || lowered.starts_with("pmid:") || lowered.starts_with("nct:") {
        cmd_source_fetch(path.trim(), None, None, false, json).await;
        // v0.102: source-fetch only retrieves metadata into a local
        // cache; it does not create frontier state. Without this hint,
        // a fresh user thinks `vela ingest doi:...` "ingested the
        // paper" because the success-shaped output looks like a
        // proposal landed. It didn't. Tell them what to do next.
        if !json {
            eprintln!();
            eprintln!(
                "  vela ingest · note: doi:/pmid:/nct: URIs only fetch metadata; no frontier state was written."
            );
            eprintln!(
                "  next: turn this paper into a proposal with `vela finding add {} --assertion '...' --author 'reviewer:you' --apply`",
                frontier.display()
            );
        }
        return;
    }

    let p = std::path::PathBuf::from(path);
    if !p.exists() {
        fail(&format!(
            "ingest: path '{path}' does not exist (and is not a doi:/pmid:/nct: URI)"
        ));
    }

    // Single-file vs folder + extension routing.
    let ext = p
        .extension()
        .and_then(|s| s.to_str())
        .map(|s| s.to_ascii_lowercase());

    if p.is_file() {
        match ext.as_deref() {
            Some("pdf") => {
                // v0.74.2: discover_files now accepts a single file
                // and returns a one-element vec, so we can pass
                // the PDF path itself directly to scout.
                cmd_scout(&p, frontier, backend, dry_run, json).await;
            }
            Some("md") | Some("markdown") => {
                // compile-notes also routes through discover_files
                // which handles the single-file case as of v0.74.2.
                cmd_compile_notes(&p, frontier, backend, None, None, dry_run, json).await;
            }
            Some("csv") | Some("tsv") => {
                // compile-data routes through discover_files; pass
                // the file path directly (v0.74.2).
                cmd_compile_data(&p, frontier, backend, None, dry_run, json).await;
            }
            Some("json") => {
                // Carina artifact packet path. Requires an actor id.
                let actor_id = actor.unwrap_or("agent:vela-ingest-bot");
                cmd_artifact_to_state(frontier, &p, actor_id, false, json);
            }
            other => {
                fail(&format!(
                    "ingest: unsupported file type '{}' (expected .pdf, .md, .csv, .tsv, .json, or a doi:/pmid:/nct: URI)",
                    other.unwrap_or("(none)")
                ));
            }
        }
        return;
    }

    if p.is_dir() {
        // v0.99: count files per handlable extension across the
        // first level. If multiple content types are present,
        // dispatch each handler in sequence rather than dropping
        // the non-dominant types silently. The previous v0.74
        // behavior picked one dominant type and ignored the rest,
        // which silently dropped mixed-source folders.
        let mut pdf_count = 0usize;
        let mut md_count = 0usize;
        let mut data_count = 0usize;
        let mut json_count = 0usize;
        let mut unhandled_exts: std::collections::BTreeSet<String> =
            std::collections::BTreeSet::new();
        if let Ok(entries) = std::fs::read_dir(&p) {
            for entry in entries.flatten() {
                let path = entry.path();
                if !path.is_file() {
                    continue;
                }
                if let Some(name) = entry.file_name().to_str()
                    && let Some(dot) = name.rfind('.')
                {
                    let ext = name[dot + 1..].to_ascii_lowercase();
                    match ext.as_str() {
                        "pdf" => pdf_count += 1,
                        "md" | "markdown" => md_count += 1,
                        "csv" | "tsv" => data_count += 1,
                        "json" => json_count += 1,
                        other => {
                            // Track the unhandled extensions so we can
                            // report them at the end. Skip dotfiles.
                            if !name.starts_with('.') {
                                unhandled_exts.insert(other.to_string());
                            }
                        }
                    }
                }
            }
        }

        let dispatched_types = (pdf_count > 0) as usize
            + (md_count > 0) as usize
            + (data_count > 0) as usize
            + (json_count > 0) as usize;

        if dispatched_types == 0 {
            // No handlable content; treat as a code repo (the
            // pre-v0.99 fallback path).
            cmd_compile_code(&p, frontier, backend, None, dry_run, json).await;
            return;
        }

        if dispatched_types > 1 {
            eprintln!(
                "  vela ingest · folder has multiple handlable types; running each in sequence"
            );
            eprintln!(
                "    pdf:{pdf_count}  md:{md_count}  csv/tsv:{data_count}  json:{json_count}"
            );
        }

        // Dispatch in a stable order: PDFs first (richest content),
        // then notes, then data, then carina packets. Each handler
        // only opens files matching its own extension via
        // discover_files; non-matching files are silently skipped
        // by the inner handler, so dispatching all four against the
        // same folder is safe and idempotent on per-extension subsets.
        if pdf_count > 0 {
            cmd_scout(&p, frontier, backend, dry_run, json).await;
        }
        if md_count > 0 {
            cmd_compile_notes(&p, frontier, backend, None, None, dry_run, json).await;
        }
        if data_count > 0 {
            cmd_compile_data(&p, frontier, backend, None, dry_run, json).await;
        }
        if json_count > 0 {
            // Carina artifact packets are file-at-a-time. Walk the
            // directory and import each .json individually.
            let actor_id = actor.unwrap_or("agent:vela-ingest-bot");
            if let Ok(entries) = std::fs::read_dir(&p) {
                for entry in entries.flatten() {
                    let path = entry.path();
                    if path.is_file()
                        && path
                            .extension()
                            .and_then(|s| s.to_str())
                            .map(|s| s.eq_ignore_ascii_case("json"))
                            .unwrap_or(false)
                    {
                        cmd_artifact_to_state(frontier, &path, actor_id, false, json);
                    }
                }
            }
        }

        if !unhandled_exts.is_empty() {
            let kinds: Vec<String> = unhandled_exts.into_iter().collect();
            eprintln!(
                "  vela ingest · skipped {} file extension(s) with no handler: {}",
                kinds.len(),
                kinds.join(", ")
            );
        }
        return;
    }

    fail(&format!(
        "ingest: path '{path}' is neither a file nor a directory"
    ));
}

#[allow(clippy::too_many_arguments)]
/// v0.25 Agent Inbox: dispatches the registered datasets handler.
async fn cmd_compile_data(
    root: &Path,
    frontier: &Path,
    backend: Option<&str>,
    sample_rows: Option<usize>,
    dry_run: bool,
    json_out: bool,
) {
    match DATASETS_HANDLER.get() {
        Some(handler) => {
            handler(
                root.to_path_buf(),
                frontier.to_path_buf(),
                backend.map(String::from),
                sample_rows,
                dry_run,
                json_out,
            )
            .await;
        }
        None => {
            eprintln!(
                "{} `vela compile-data` requires the vela CLI binary; the library is unwired without a registered datasets handler.",
                style::err_prefix()
            );
            std::process::exit(1);
        }
    }
}

/// v0.28 Agent Inbox: dispatches the registered reviewer-agent
/// handler.
async fn cmd_review_pending(
    frontier: &Path,
    backend: Option<&str>,
    max_proposals: Option<usize>,
    batch_size: usize,
    dry_run: bool,
    json_out: bool,
) {
    match REVIEWER_HANDLER.get() {
        Some(handler) => {
            handler(
                frontier.to_path_buf(),
                backend.map(String::from),
                max_proposals,
                batch_size,
                dry_run,
                json_out,
            )
            .await;
        }
        None => {
            eprintln!(
                "{} `vela review-pending` requires the vela CLI binary; the library is unwired without a registered reviewer handler.",
                style::err_prefix()
            );
            std::process::exit(1);
        }
    }
}

/// v0.28 Agent Inbox: dispatches the registered contradiction-finder
/// handler.
async fn cmd_find_tensions(
    frontier: &Path,
    backend: Option<&str>,
    max_findings: Option<usize>,
    dry_run: bool,
    json_out: bool,
) {
    match TENSIONS_HANDLER.get() {
        Some(handler) => {
            handler(
                frontier.to_path_buf(),
                backend.map(String::from),
                max_findings,
                dry_run,
                json_out,
            )
            .await;
        }
        None => {
            eprintln!(
                "{} `vela find-tensions` requires the vela CLI binary; the library is unwired without a registered tensions handler.",
                style::err_prefix()
            );
            std::process::exit(1);
        }
    }
}

/// v0.28 Agent Inbox: dispatches the registered experiment-planner
/// handler.
async fn cmd_plan_experiments(
    frontier: &Path,
    backend: Option<&str>,
    max_findings: Option<usize>,
    dry_run: bool,
    json_out: bool,
) {
    match EXPERIMENTS_HANDLER.get() {
        Some(handler) => {
            handler(
                frontier.to_path_buf(),
                backend.map(String::from),
                max_findings,
                dry_run,
                json_out,
            )
            .await;
        }
        None => {
            eprintln!(
                "{} `vela plan-experiments` requires the vela CLI binary; the library is unwired without a registered experiments handler.",
                style::err_prefix()
            );
            std::process::exit(1);
        }
    }
}

/// v0.24 Agent Inbox: dispatches the registered code-analyst
/// handler.
async fn cmd_compile_code(
    root: &Path,
    frontier: &Path,
    backend: Option<&str>,
    max_files: Option<usize>,
    dry_run: bool,
    json_out: bool,
) {
    match CODE_HANDLER.get() {
        Some(handler) => {
            handler(
                root.to_path_buf(),
                frontier.to_path_buf(),
                backend.map(String::from),
                max_files,
                dry_run,
                json_out,
            )
            .await;
        }
        None => {
            eprintln!(
                "{} `vela compile-code` requires the vela CLI binary; the library is unwired without a registered code handler.",
                style::err_prefix()
            );
            std::process::exit(1);
        }
    }
}

/// v0.23 Agent Inbox: dispatches the registered notes-compiler
/// handler. Same rationale as `cmd_scout` — the substrate stays
/// agent-free; the `vela` CLI binary registers the handler at
/// startup.
async fn cmd_compile_notes(
    vault: &Path,
    frontier: &Path,
    backend: Option<&str>,
    max_files: Option<usize>,
    max_items_per_category: Option<usize>,
    dry_run: bool,
    json_out: bool,
) {
    match NOTES_HANDLER.get() {
        Some(handler) => {
            handler(
                vault.to_path_buf(),
                frontier.to_path_buf(),
                backend.map(String::from),
                max_files,
                max_items_per_category,
                dry_run,
                json_out,
            )
            .await;
        }
        None => {
            eprintln!(
                "{} `vela compile-notes` requires the vela CLI binary; the library is unwired without a registered notes handler.",
                style::err_prefix()
            );
            std::process::exit(1);
        }
    }
}

/// v0.22 Agent Inbox: dispatches the registered scout handler. The
/// substrate library does not import `vela-scientist` (it would induce
/// a Cargo cycle); the `vela` CLI binary in `crates/vela-cli`
/// registers a handler at startup that calls into the scientist
/// crate. Running the lib directly without that registration prints
/// a clear error.
async fn cmd_scout(
    folder: &Path,
    frontier: &Path,
    backend: Option<&str>,
    dry_run: bool,
    json_out: bool,
) {
    match SCOUT_HANDLER.get() {
        Some(handler) => {
            handler(
                folder.to_path_buf(),
                frontier.to_path_buf(),
                backend.map(String::from),
                dry_run,
                json_out,
            )
            .await;
        }
        None => {
            eprintln!(
                "{} `vela scout` requires the vela CLI binary; the library is unwired without a registered scout handler.",
                style::err_prefix()
            );
            std::process::exit(1);
        }
    }
}

#[allow(clippy::too_many_arguments)]
fn cmd_check(
    source: Option<&Path>,
    schema: bool,
    stats: bool,
    conformance_flag: bool,
    conformance_dir: &Path,
    all: bool,
    schema_only: bool,
    strict: bool,
    fix: bool,
    json_output: bool,
) {
    if json_output {
        let Some(src) = source else {
            fail("--json requires a frontier source");
        };
        let payload = check_json_payload(src, schema_only, strict);
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize check report")
        );
        if payload.get("ok").and_then(Value::as_bool) != Some(true) {
            std::process::exit(1);
        }
        return;
    }

    let run_all = all || (!schema && !stats && !conformance_flag && !schema_only);
    if run_all || schema || schema_only {
        let Some(src) = source else {
            fail("check requires a frontier source");
        };
        validate::run(src);
    }
    if !schema_only && (run_all || stats) {
        let Some(src) = source else {
            fail("--stats requires a frontier source");
        };
        let frontier = load_frontier_or_fail(src);
        let report = lint::lint(&frontier, None, None);
        lint::print_report(&report);
        let replay_report = events::replay_report(&frontier);
        println!("event replay: {}", replay_report.status);
        if !replay_report.conflicts.is_empty() {
            for conflict in &replay_report.conflicts {
                println!("  - {conflict}");
            }
        }
        if let Ok(signature_report) = sign::verify_frontier_data(&frontier, None)
            && signature_report.signed > 0
        {
            println!(
                "Signatures: {} valid / {} invalid / {} unsigned",
                signature_report.valid, signature_report.invalid, signature_report.unsigned
            );
        }
        let signal_report = signals::analyze(&frontier, &[]);
        print_signal_summary(&signal_report, strict);
        if !replay_report.ok
            || (strict
                && (!signal_report.review_queue.is_empty()
                    || signal_report.proof_readiness.status != "ready"))
        {
            std::process::exit(1);
        }
    }
    if run_all || conformance_flag {
        // v0.106: a fresh `cargo install vela-cli` user runs `vela check`
        // from a directory without `tests/conformance/` (those vectors
        // live in the source repo). Pre-v0.106 the default
        // `run_all` path called `conformance::run` unconditionally,
        // which `process::exit(1)`'d with a confusing error. Skip
        // gracefully when the conformance dir is missing AND the
        // user did not pass `--conformance` explicitly. The
        // explicit `--conformance` flag still errors, which is the
        // right behavior for someone who asked for it.
        if conformance_flag || conformance_dir.is_dir() {
            conformance::run(conformance_dir);
        } else {
            eprintln!(
                "  conformance: skipped ({} not present; pass --conformance-dir <path> to point at the source repo's tests/conformance)",
                conformance_dir.display()
            );
        }
    }
    let _ = fix;
}

fn check_json_payload(src: &Path, schema_only: bool, strict: bool) -> Value {
    let report = validate::validate(src);
    let loaded = repo::load_from_path(src).ok();
    let (method_report, graph_report) = if schema_only {
        (None, None)
    } else if let Some(frontier) = loaded.as_ref() {
        (
            Some(lint::lint(frontier, None, None)),
            Some(lint::lint_frontier(frontier)),
        )
    } else {
        (None, None)
    };
    let source_hash = hash_path(src).unwrap_or_else(|_| "unavailable".to_string());
    let mut diagnostics = Vec::new();
    diagnostics.extend(report.errors.iter().map(|e| {
        json!({
            "severity": "error",
            "rule_id": "schema",
            "finding_id": null,
            "file": &e.file,
            "field_path": null,
            "message": &e.error,
            "suggestion": schema_error_suggestion(&e.error),
            "fixable": schema_error_fix(&e.error),
            "normalize_action": schema_error_action(&e.error),
        })
    }));
    for (check_id, lint_report) in [
        ("methodology", method_report.as_ref()),
        ("frontier_graph", graph_report.as_ref()),
    ] {
        if let Some(lint_report) = lint_report {
            diagnostics.extend(lint_report.diagnostics.iter().map(|d| {
                json!({
                    "severity": d.severity.to_string(),
                    "rule_id": &d.rule_id,
                    "check": check_id,
                    "finding_id": &d.finding_id,
                    "field_path": null,
                    "message": &d.message,
                    "suggestion": &d.suggestion,
                    "fixable": false,
                    "normalize_action": null,
                })
            }));
        }
    }
    let method_errors = method_report.as_ref().map_or(0, |r| r.errors);
    let method_warnings = method_report.as_ref().map_or(0, |r| r.warnings);
    let method_infos = method_report.as_ref().map_or(0, |r| r.infos);
    let graph_errors = graph_report.as_ref().map_or(0, |r| r.errors);
    let graph_warnings = graph_report.as_ref().map_or(0, |r| r.warnings);
    let graph_infos = graph_report.as_ref().map_or(0, |r| r.infos);
    let replay_report = loaded.as_ref().map(events::replay_report);
    let state_integrity_report = if schema_only {
        loaded.as_ref().map(state_integrity::analyze)
    } else {
        state_integrity::analyze_path(src).ok()
    };
    if let Some(replay) = replay_report.as_ref()
        && !replay.ok
    {
        diagnostics.extend(replay.conflicts.iter().map(|conflict| {
            json!({
                "severity": "error",
                "rule_id": "event_replay",
                "check": "events",
                "finding_id": null,
                "field_path": null,
                "message": conflict,
                "suggestion": "Inspect canonical state events and repair the frontier event log before proof export.",
                "fixable": false,
                "normalize_action": null,
            })
        }));
    }
    let event_errors = replay_report
        .as_ref()
        .map_or(0, |replay| usize::from(!replay.ok));
    let state_integrity_errors = state_integrity_report
        .as_ref()
        .map_or(0, |report| report.structural_errors.len());
    let (source_registry, evidence_atoms, conditions, proposal_summary, proof_state) = loaded
        .as_ref()
        .map(|frontier| {
            (
                sources::source_summary(frontier),
                sources::evidence_summary(frontier),
                sources::condition_summary(frontier),
                proposals::summary(frontier),
                proposals::proof_state_json(&frontier.proof_state),
            )
        })
        .unwrap_or_else(|| {
            (
                sources::SourceRegistrySummary::default(),
                sources::EvidenceAtomSummary::default(),
                sources::ConditionSummary::default(),
                proposals::ProposalSummary::default(),
                Value::Null,
            )
        });
    let signature_report = loaded
        .as_ref()
        .and_then(|frontier| sign::verify_frontier_data(frontier, None).ok());
    if let Some(frontier) = loaded.as_ref()
        && !schema_only
    {
        let projection = sources::derive_projection(frontier);
        let existing_sources = frontier
            .sources
            .iter()
            .map(|source| source.id.as_str())
            .collect::<std::collections::BTreeSet<_>>();
        let existing_atoms = frontier
            .evidence_atoms
            .iter()
            .map(|atom| atom.id.as_str())
            .collect::<std::collections::BTreeSet<_>>();
        let existing_conditions = frontier
            .condition_records
            .iter()
            .map(|record| record.id.as_str())
            .collect::<std::collections::BTreeSet<_>>();
        for source in projection
            .sources
            .iter()
            .filter(|source| !existing_sources.contains(source.id.as_str()))
        {
            diagnostics.push(json!({
                "severity": "warning",
                "rule_id": "missing_source_record",
                "check": "source_registry",
                "finding_id": source.finding_ids.first(),
                "field_path": "sources",
                "message": format!("Source record {} is derivable but not materialized in frontier state.", source.id),
                "suggestion": "Run `vela normalize` to materialize source records before proof export.",
                "fixable": true,
                "normalize_action": "materialize_source_record",
            }));
        }
        for atom in projection
            .evidence_atoms
            .iter()
            .filter(|atom| !existing_atoms.contains(atom.id.as_str()))
        {
            diagnostics.push(json!({
                "severity": "warning",
                "rule_id": "missing_evidence_atom",
                "check": "evidence_atoms",
                "finding_id": atom.finding_id,
                "field_path": "evidence_atoms",
                "message": format!("Evidence atom {} is derivable but not materialized in frontier state.", atom.id),
                "suggestion": "Run `vela normalize` to materialize evidence atoms before proof export.",
                "fixable": true,
                "normalize_action": "materialize_evidence_atom",
            }));
        }
        for atom in projection
            .evidence_atoms
            .iter()
            .filter(|atom| atom.locator.is_none())
        {
            diagnostics.push(json!({
                "severity": "warning",
                "rule_id": "missing_evidence_locator",
                "check": "evidence_atoms",
                "finding_id": atom.finding_id,
                "field_path": "evidence_atoms[].locator",
                "message": format!("Evidence atom {} has no source locator.", atom.id),
                "suggestion": "Add or verify evidence spans, table rows, pages, sections, or run locators.",
                "fixable": false,
                "normalize_action": null,
            }));
        }
        for condition in projection
            .condition_records
            .iter()
            .filter(|condition| !existing_conditions.contains(condition.id.as_str()))
        {
            diagnostics.push(json!({
                "severity": "warning",
                "rule_id": "condition_record_missing",
                "check": "conditions",
                "finding_id": condition.finding_id,
                "field_path": "condition_records",
                "message": format!("Condition record {} is derivable but not materialized in frontier state.", condition.id),
                "suggestion": "Run `vela normalize` to materialize condition boundaries before proof export.",
                "fixable": true,
                "normalize_action": "materialize_condition_record",
            }));
        }
        for proposal in frontier.proposals.iter().filter(|proposal| {
            matches!(proposal.status.as_str(), "accepted" | "applied")
                && proposal
                    .reviewed_by
                    .as_deref()
                    .is_none_or(proposals::is_placeholder_reviewer)
        }) {
            diagnostics.push(json!({
                "severity": "error",
                "rule_id": "reviewer_identity_missing",
                "check": "proposals",
                "finding_id": proposal.target.id,
                "field_path": "proposals[].reviewed_by",
                "message": format!("Accepted or applied proposal {} uses a missing or placeholder reviewer identity.", proposal.id),
                "suggestion": "Accept the proposal with a stable named reviewer id before strict proof use.",
                "fixable": false,
                "normalize_action": null,
            }));
        }
    }
    let signal_report = loaded
        .as_ref()
        .map(|frontier| signals::analyze(frontier, &diagnostics))
        .unwrap_or_else(empty_signal_report);
    let errors =
        report.errors.len() + method_errors + graph_errors + event_errors + state_integrity_errors;
    let warnings = method_warnings + graph_warnings + signal_report.proof_readiness.warnings;
    let infos = method_infos + graph_infos;
    let strict_blockers = signal_report
        .signals
        .iter()
        .filter(|signal| signal.blocks.iter().any(|block| block == "strict_check"))
        .count();
    let fixable = diagnostics
        .iter()
        .filter(|d| d.get("fixable").and_then(Value::as_bool).unwrap_or(false))
        .count();
    let ok = errors == 0 && (!strict || (warnings == 0 && strict_blockers == 0));

    json!({
        "ok": ok,
        "command": "check",
        "schema_version": project::VELA_SCHEMA_VERSION,
        "source": {
            "path": src.display().to_string(),
            "hash": format!("sha256:{source_hash}"),
        },
        "summary": {
            "status": if ok { "pass" } else { "fail" },
            "checked_findings": report.total_files,
            "valid_findings": report.valid,
            "invalid_findings": report.invalid,
            "errors": errors,
            "warnings": warnings,
            "info": infos,
            "fixable": fixable,
            "strict": strict,
            "schema_only": schema_only,
        },
        "checks": [
            {
                "id": "schema",
                "status": if report.invalid == 0 { "pass" } else { "fail" },
                "checked": report.total_files,
                "failed": report.invalid,
                "errors": report.errors.iter().map(|e| json!({
                    "file": e.file,
                    "message": e.error,
                })).collect::<Vec<_>>(),
            },
            {
                "id": "methodology",
                "status": if method_errors == 0 { "pass" } else { "fail" },
                "checked": method_report.as_ref().map_or(0, |r| r.findings_checked),
                "failed": method_errors,
                "warnings": method_warnings,
                "info": method_infos,
                "skipped": schema_only,
            },
            {
                "id": "frontier_graph",
                "status": if graph_errors == 0 { "pass" } else { "fail" },
                "checked": graph_report.as_ref().map_or(0, |r| r.findings_checked),
                "failed": graph_errors,
                "warnings": graph_warnings,
                "info": graph_infos,
                "skipped": schema_only,
            },
            {
                "id": "signals",
                "status": if strict_blockers == 0 { "pass" } else { "fail" },
                "checked": signal_report.signals.len(),
                "failed": strict_blockers,
                "warnings": signal_report.proof_readiness.warnings,
                "skipped": loaded.is_none(),
                "blockers": signal_report.signals.iter()
                    .filter(|s| s.blocks.iter().any(|b| b == "strict_check"))
                    .map(|s| json!({
                        "id": s.id,
                        "kind": s.kind,
                        "severity": s.severity,
                        "reason": s.reason,
                    }))
                    .collect::<Vec<_>>(),
            },
            {
                "id": "events",
                "status": if replay_report.as_ref().is_none_or(|replay| replay.ok) { "pass" } else { "fail" },
                "checked": replay_report.as_ref().map_or(0, |replay| replay.event_log.count),
                "failed": event_errors,
                "skipped": schema_only || loaded.is_none(),
            },
            {
                "id": "state_integrity",
                "status": if state_integrity_report.as_ref().is_none_or(|report| report.status != "fail") { "pass" } else { "fail" },
                "checked": state_integrity_report.as_ref().map_or(0, |report| report.summary.get("events").copied().unwrap_or_default()),
                "failed": state_integrity_errors,
                "skipped": schema_only || loaded.is_none(),
            }
        ],
        "event_log": replay_report.as_ref().map(|replay| &replay.event_log),
        "replay": replay_report,
        "state_integrity": state_integrity_report,
        "source_registry": source_registry,
        "evidence_atoms": evidence_atoms,
        "conditions": conditions,
        "proposals": proposal_summary,
        "proof_state": proof_state,
        "signatures": signature_report,
        "diagnostics": diagnostics,
        "signals": signal_report.signals,
        "review_queue": signal_report.review_queue,
        "proof_readiness": signal_report.proof_readiness,
        "repair_plan": build_repair_plan(&diagnostics),
    })
}

#[allow(clippy::too_many_arguments)]
fn cmd_normalize(
    source: &Path,
    out: Option<&Path>,
    write: bool,
    dry_run: bool,
    rewrite_ids: bool,
    id_map: Option<&Path>,
    resync_provenance: bool,
    json_output: bool,
) {
    if write && out.is_some() {
        fail("Use either --write or --out, not both.");
    }
    if dry_run && (write || out.is_some()) {
        fail("--dry-run cannot be combined with --write or --out.");
    }
    if id_map.is_some() && !rewrite_ids {
        fail("--id-map requires --rewrite-ids.");
    }

    let detected = repo::detect(source).unwrap_or_else(|e| {
        eprintln!("{e}");
        std::process::exit(1);
    });
    if matches!(detected, repo::VelaSource::PacketDir(_)) {
        fail(
            "Cannot normalize a proof packet directory. Export a new packet from frontier state instead.",
        );
    }
    let mut frontier = repo::load(&detected).unwrap_or_else(|e| fail_return(&e));
    // Phase J: every v0.4 frontier carries a `frontier.created` genesis
    // event in events[0]. That's identity metadata, not a substantive
    // mutation, so it doesn't disqualify normalization. Any non-genesis
    // canonical event still blocks normalize.
    let has_substantive_events = frontier
        .events
        .iter()
        .any(|event| event.kind != "frontier.created");
    if has_substantive_events && (write || out.is_some()) {
        fail(
            "Refusing to normalize a frontier with canonical events. Normalize before proposal-backed writes, or create a new reviewed transition for the intended change.",
        );
    }
    let source_hash = hash_path(source).unwrap_or_else(|_| "unavailable".to_string());
    let before_stats = serde_json::to_value(&frontier.stats).unwrap_or(Value::Null);
    let (entity_type_fixes, entity_name_fixes) =
        normalize::normalize_findings(&mut frontier.findings);
    let confidence_updates =
        bundle::recompute_all_confidence(&mut frontier.findings, &frontier.replications);
    // Phase N: optionally rewrite finding.provenance from the canonical
    // SourceRecord. The source registry is the authority; provenance is
    // the denormalized cache.
    let provenance_resync_count = if resync_provenance {
        sources::resync_provenance_from_sources(&mut frontier)
    } else {
        0
    };
    let before_source_count = frontier.sources.len();
    let before_evidence_atom_count = frontier.evidence_atoms.len();
    let before_condition_record_count = frontier.condition_records.len();

    let mut id_rewrites = Vec::new();
    if rewrite_ids {
        let mut id_map_values = std::collections::BTreeMap::<String, String>::new();
        for finding in &frontier.findings {
            let expected =
                bundle::FindingBundle::content_address(&finding.assertion, &finding.provenance);
            if expected != finding.id {
                id_map_values.insert(finding.id.clone(), expected);
            }
        }
        let new_ids = id_map_values
            .values()
            .map(String::as_str)
            .collect::<std::collections::HashSet<_>>();
        if new_ids.len() != id_map_values.len() {
            fail("Refusing to rewrite IDs because two findings map to the same content address.");
        }
        for finding in &mut frontier.findings {
            if let Some(new_id) = id_map_values.get(&finding.id) {
                id_rewrites.push(json!({"old": finding.id, "new": new_id}));
                finding.previous_version = Some(finding.id.clone());
                finding.id = new_id.clone();
            }
        }
        for finding in &mut frontier.findings {
            for link in &mut finding.links {
                if let Some(new_target) = id_map_values.get(&link.target) {
                    link.target = new_target.clone();
                }
            }
        }
        if let Some(path) = id_map {
            std::fs::write(
                path,
                serde_json::to_string_pretty(&id_map_values)
                    .expect("failed to serialize normalize id map"),
            )
            .unwrap_or_else(|e| fail(&format!("Failed to write {}: {e}", path.display())));
        }
    }

    sources::materialize_project(&mut frontier);
    let source_records_materialized = frontier.sources.len().saturating_sub(before_source_count);
    let evidence_atoms_materialized = frontier
        .evidence_atoms
        .len()
        .saturating_sub(before_evidence_atom_count);
    let condition_records_materialized = frontier
        .condition_records
        .len()
        .saturating_sub(before_condition_record_count);
    let after_stats = serde_json::to_value(&frontier.stats).unwrap_or(Value::Null);
    let id_rewrite_count = id_rewrites.len();
    let wrote_to = if write {
        repo::save(&detected, &frontier).unwrap_or_else(|e| fail(&e));
        Some(source.display().to_string())
    } else if let Some(out_path) = out {
        repo::save_to_path(out_path, &frontier).unwrap_or_else(|e| fail(&e));
        Some(out_path.display().to_string())
    } else {
        None
    };
    let wrote = wrote_to.is_some();
    let planned_changes = entity_type_fixes
        + entity_name_fixes
        + confidence_updates
        + id_rewrite_count
        + source_records_materialized
        + evidence_atoms_materialized
        + condition_records_materialized
        + provenance_resync_count;
    let payload = json!({
        "ok": true,
        "command": "normalize",
        "schema_version": project::VELA_SCHEMA_VERSION,
        "source": {
            "path": source.display().to_string(),
            "hash": format!("sha256:{source_hash}"),
        },
        "dry_run": wrote_to.is_none(),
        "wrote_to": wrote_to,
        "summary": {
            "planned": planned_changes,
            "safe": planned_changes,
            "unsafe": 0,
            "applied": if wrote { planned_changes } else { 0 },
        },
        "changes": {
            "entity_type_fixes": entity_type_fixes,
            "entity_name_fixes": entity_name_fixes,
            "confidence_updates": confidence_updates,
            "id_rewrites": id_rewrite_count,
            "source_records_materialized": source_records_materialized,
            "evidence_atoms_materialized": evidence_atoms_materialized,
            "condition_records_materialized": condition_records_materialized,
            "provenance_resyncs": provenance_resync_count,
            "stats_changed": before_stats != after_stats,
        },
        "id_rewrites": id_rewrites,
        "repair_plan": if wrote { Vec::<Value>::new() } else {
            vec![json!({
                "action": "apply_normalization",
                "command": "vela normalize <frontier> --out frontier.normalized.json"
            })]
        },
    });
    if json_output {
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize normalize report")
        );
    } else if let Some(path) = payload.get("wrote_to").and_then(Value::as_str) {
        println!("{} normalized frontier written to {path}", style::ok("ok"));
        println!(
            "  entity type fixes: {}, entity name fixes: {}, confidence updates: {}, id rewrites: {}",
            entity_type_fixes, entity_name_fixes, confidence_updates, id_rewrite_count
        );
    } else {
        println!("normalize dry run for {}", source.display());
        println!(
            "  would apply entity type fixes: {}, entity name fixes: {}, confidence updates: {}, id rewrites: {}",
            entity_type_fixes, entity_name_fixes, confidence_updates, id_rewrite_count
        );
    }
}

fn cmd_proof(
    frontier: &Path,
    out: &Path,
    template: &str,
    gold: Option<&Path>,
    record_proof_state: bool,
    json_output: bool,
) {
    if template != "bbb-alzheimer" {
        fail(&format!(
            "Unsupported proof template '{template}'. Supported: bbb-alzheimer"
        ));
    }
    let mut loaded = load_frontier_or_fail(frontier);
    let source_hash = hash_path_or_fail(frontier);
    let export_record = export::export_packet_with_source(&loaded, Some(frontier), out)
        .unwrap_or_else(|e| fail(&e));
    let benchmark_summary = gold.map(|gold_path| {
        let summary = benchmark::run_suite(gold_path).unwrap_or_else(|e| {
            fail(&format!(
                "Failed to run proof benchmark '{}': {e}",
                gold_path.display()
            ))
        });
        append_packet_json_file(out, "benchmark-summary.json", &summary).unwrap_or_else(|e| {
            fail(&format!("Failed to write benchmark summary: {e}"));
        });
        if summary.get("ok").and_then(Value::as_bool) != Some(true) {
            fail(&format!(
                "Proof benchmark failed for {}",
                gold_path.display()
            ));
        }
        summary
    });
    let validation_summary = packet::validate(out).unwrap_or_else(|e| {
        fail(&format!("Proof packet validation failed: {e}"));
    });
    proposals::record_proof_export(
        &mut loaded,
        proposals::ProofPacketRecord {
            generated_at: export_record.generated_at.clone(),
            snapshot_hash: export_record.snapshot_hash.clone(),
            event_log_hash: export_record.event_log_hash.clone(),
            packet_manifest_hash: export_record.packet_manifest_hash.clone(),
        },
    );
    project::recompute_stats(&mut loaded);
    if record_proof_state {
        repo::save_to_path(frontier, &loaded).unwrap_or_else(|e| fail(&e));
    }
    let signal_report = signals::analyze(&loaded, &[]);
    if json_output {
        let payload = json!({
            "ok": true,
            "command": "proof",
            "schema_version": project::VELA_SCHEMA_VERSION,
            "recorded_proof_state": record_proof_state,
            "frontier": {
                "name": &loaded.project.name,
                "source": frontier.display().to_string(),
                "hash": format!("sha256:{source_hash}"),
            },
            "template": template,
            "gold": gold.map(|p| p.display().to_string()),
            "benchmark": benchmark_summary,
            "output": out.display().to_string(),
            "packet": {
                "manifest_path": out.join("manifest.json").display().to_string(),
            },
            "validation": {
                "status": "ok",
                "summary": validation_summary,
            },
            "proposals": proposals::summary(&loaded),
            "proof_state": loaded.proof_state,
            "signals": signal_report.signals,
            "review_queue": signal_report.review_queue,
            "proof_readiness": signal_report.proof_readiness,
            "trace_path": out.join("proof-trace.json").display().to_string(),
        });
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize proof response")
        );
    } else {
        println!("vela proof");
        println!("  source:   {}", frontier.display());
        println!("  template: {template}");
        println!("  output:   {}", out.display());
        println!("  trace:    {}", out.join("proof-trace.json").display());
        println!(
            "  proof state: {}",
            if record_proof_state {
                "recorded"
            } else {
                "not recorded"
            }
        );
        println!();
        println!("{validation_summary}");
    }
}

// ── v0.42 daily-driver triad ────────────────────────────────────────

/// v0.42: One-screen status. The `git status` analogue.
fn cmd_status(path: &Path, json: bool) {
    let project = repo::load_from_path(path).unwrap_or_else(|e| fail_return(&e));

    // Inbox counts.
    let mut pending_total = 0usize;
    let mut pending_by_kind: std::collections::BTreeMap<String, usize> =
        std::collections::BTreeMap::new();
    for p in &project.proposals {
        if p.status == "pending_review" {
            pending_total += 1;
            *pending_by_kind.entry(p.kind.clone()).or_insert(0) += 1;
        }
    }

    // Causal audit summary.
    let audit = crate::causal_reasoning::audit_frontier(&project);
    let audit_summary = crate::causal_reasoning::summarize_audit(&audit);

    // Federation health: peers + last sync.
    let mut last_sync: Option<&crate::events::StateEvent> = None;
    let mut last_conflict: Option<&crate::events::StateEvent> = None;
    let mut total_conflicts = 0usize;
    for e in &project.events {
        match e.kind.as_str() {
            "frontier.synced_with_peer" => {
                if last_sync
                    .map(|prev| e.timestamp > prev.timestamp)
                    .unwrap_or(true)
                {
                    last_sync = Some(e);
                }
            }
            "frontier.conflict_detected" => {
                total_conflicts += 1;
                if last_conflict
                    .map(|prev| e.timestamp > prev.timestamp)
                    .unwrap_or(true)
                {
                    last_conflict = Some(e);
                }
            }
            _ => {}
        }
    }

    // Replication health.
    let mut targets_with_success = std::collections::HashSet::new();
    let mut failed_replications = 0usize;
    for r in &project.replications {
        if r.outcome == "replicated" {
            targets_with_success.insert(r.target_finding.clone());
        } else if r.outcome == "failed" {
            failed_replications += 1;
        }
    }

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "status",
                "frontier": frontier_label(&project),
                "vfr_id": project.frontier_id(),
                "findings": project.findings.len(),
                "events": project.events.len(),
                "actors": project.actors.len(),
                "peers": project.peers.len(),
                "inbox": {
                    "pending_total": pending_total,
                    "pending_by_kind": pending_by_kind,
                },
                "causal_audit": {
                    "identified": audit_summary.identified,
                    "conditional": audit_summary.conditional,
                    "underidentified": audit_summary.underidentified,
                    "underdetermined": audit_summary.underdetermined,
                },
                "replications": {
                    "total": project.replications.len(),
                    "findings_with_success": targets_with_success.len(),
                    "failed": failed_replications,
                },
                "federation": {
                    "peers": project.peers.len(),
                    "last_sync": last_sync.map(|e| e.timestamp.clone()),
                    "last_conflict": last_conflict.map(|e| e.timestamp.clone()),
                    "total_conflicts": total_conflicts,
                },
            }))
            .expect("serialize status")
        );
        return;
    }

    println!();
    println!(
        "  {}",
        format!("VELA · STATUS · {}", path.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    println!();
    println!("  frontier:    {}", frontier_label(&project));
    println!("  vfr_id:      {}", project.frontier_id());
    println!(
        "  findings:    {}    events: {}    peers: {}    actors: {}",
        project.findings.len(),
        project.events.len(),
        project.peers.len(),
        project.actors.len(),
    );
    println!();
    if pending_total > 0 {
        println!(
            "  {}  {pending_total} pending proposals",
            style::warn("inbox")
        );
        for (k, n) in &pending_by_kind {
            println!("    · {n:>3}  {k}");
        }
    } else {
        println!("  {}  inbox clean", style::ok("ok"));
    }
    println!();
    if audit_summary.underidentified > 0 || audit_summary.conditional > 0 {
        let chip = if audit_summary.underidentified > 0 {
            style::lost("audit")
        } else {
            style::warn("audit")
        };
        println!(
            "  {}  identified {} · conditional {} · underidentified {} · underdetermined {}",
            chip,
            audit_summary.identified,
            audit_summary.conditional,
            audit_summary.underidentified,
            audit_summary.underdetermined,
        );
        if audit_summary.underidentified > 0 {
            println!(
                "    next: vela causal audit {} --problems-only",
                path.display()
            );
        }
    } else if audit_summary.underdetermined == 0 {
        println!(
            "  {}  causal audit: all {} identified",
            style::ok("ok"),
            audit_summary.identified
        );
    } else {
        println!(
            "  {}  causal audit: {} identified, {} ungraded",
            style::warn("audit"),
            audit_summary.identified,
            audit_summary.underdetermined,
        );
    }
    println!();
    if !project.replications.is_empty() {
        println!(
            "  {}  {} records · {} findings replicated · {} failed",
            style::ok("replications"),
            project.replications.len(),
            targets_with_success.len(),
            failed_replications,
        );
    }
    if project.peers.is_empty() {
        println!(
            "  {}  no federation peers registered",
            style::warn("federation")
        );
    } else {
        let last = last_sync
            .map(|e| fmt_timestamp(&e.timestamp))
            .unwrap_or_else(|| "never".to_string());
        let chip = if total_conflicts > 0 {
            style::warn("federation")
        } else {
            style::ok("federation")
        };
        println!(
            "  {}  {} peer(s) · last sync {} · {} conflict events",
            chip,
            project.peers.len(),
            last,
            total_conflicts,
        );
    }
    println!();
}

/// v0.42: Recent canonical events. The `git log` analogue.
fn cmd_log(path: &Path, limit: usize, kind_filter: Option<&str>, json: bool) {
    let project = repo::load_from_path(path).unwrap_or_else(|e| fail_return(&e));
    let mut events: Vec<&crate::events::StateEvent> = project
        .events
        .iter()
        .filter(|e| match kind_filter {
            Some(k) => e.kind.contains(k),
            None => true,
        })
        .collect();
    events.sort_by(|a, b| b.timestamp.cmp(&a.timestamp));
    events.truncate(limit);

    if json {
        let payload: Vec<_> = events
            .iter()
            .map(|e| {
                json!({
                    "id": e.id,
                    "kind": e.kind,
                    "actor": e.actor.id,
                    "target": &e.target.id,
                    "target_type": &e.target.r#type,
                    "timestamp": e.timestamp,
                    "reason": e.reason,
                })
            })
            .collect();
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "log",
                "events": payload,
            }))
            .expect("serialize log")
        );
        return;
    }

    println!();
    println!(
        "  {}",
        format!("VELA · LOG · {}  (latest {})", path.display(), events.len())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if events.is_empty() {
        println!("  (no events)");
        return;
    }
    for e in &events {
        let when = fmt_timestamp(&e.timestamp);
        let target_short = if e.target.id.len() > 22 {
            format!("{}…", &e.target.id[..21])
        } else {
            e.target.id.clone()
        };
        let reason: String = e.reason.chars().take(70).collect();
        println!(
            "  {:<19}  {:<32}  {:<24}  {}",
            when, e.kind, target_short, reason
        );
    }
    println!();
}

/// v0.42: Pending-proposals triage. The thing you sit down to review.
fn cmd_inbox(path: &Path, kind_filter: Option<&str>, limit: usize, json: bool) {
    let project = repo::load_from_path(path).unwrap_or_else(|e| fail_return(&e));

    // Collect reviewer-agent score map (composite shown alongside each
    // proposal where present).
    let mut score_map: std::collections::HashMap<String, (f64, f64, f64, f64)> =
        std::collections::HashMap::new();
    for p in &project.proposals {
        if p.kind != "finding.note" {
            continue;
        }
        if p.actor.id != "agent:reviewer-agent" {
            continue;
        }
        let reason = &p.reason;
        let Some(target) = reason.split_whitespace().find(|s| s.starts_with("vpr_")) else {
            continue;
        };
        let text = p.payload.get("text").and_then(|v| v.as_str()).unwrap_or("");
        let extract = |k: &str| -> f64 {
            let pat = format!("{k} ");
            text.find(&pat)
                .and_then(|idx| text[idx + pat.len()..].split_whitespace().next())
                .and_then(|t| t.parse::<f64>().ok())
                .unwrap_or(0.0)
        };
        score_map.insert(
            target.to_string(),
            (
                extract("plausibility"),
                extract("evidence"),
                extract("scope"),
                extract("duplicate-risk"),
            ),
        );
    }

    let mut pending: Vec<&crate::proposals::StateProposal> = project
        .proposals
        .iter()
        .filter(|p| {
            p.status == "pending_review"
                && match kind_filter {
                    Some(k) => p.kind.contains(k),
                    None => true,
                }
        })
        .collect();
    // Sort: high reviewer-agent composite first, then untyped.
    pending.sort_by(|a, b| {
        let sa = score_map
            .get(&a.id)
            .map(|(p, e, s, d)| 0.4 * p + 0.3 * e + 0.2 * s - 0.3 * d);
        let sb = score_map
            .get(&b.id)
            .map(|(p, e, s, d)| 0.4 * p + 0.3 * e + 0.2 * s - 0.3 * d);
        sb.partial_cmp(&sa).unwrap_or(std::cmp::Ordering::Equal)
    });
    pending.truncate(limit);

    if json {
        let payload: Vec<_> = pending
            .iter()
            .map(|p| {
                let assertion_text = p
                    .payload
                    .get("finding")
                    .and_then(|f| f.get("assertion"))
                    .and_then(|a| a.get("text"))
                    .and_then(|t| t.as_str());
                let assertion_type = p
                    .payload
                    .get("finding")
                    .and_then(|f| f.get("assertion"))
                    .and_then(|a| a.get("type"))
                    .and_then(|t| t.as_str());
                let composite = score_map
                    .get(&p.id)
                    .map(|(pl, e, s, d)| 0.4 * pl + 0.3 * e + 0.2 * s - 0.3 * d);
                json!({
                    "proposal_id": p.id,
                    "kind": p.kind,
                    "actor": p.actor,
                    "reason": p.reason,
                    "assertion_text": assertion_text,
                    "assertion_type": assertion_type,
                    "reviewer_composite": composite,
                })
            })
            .collect();
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "inbox",
                "shown": pending.len(),
                "proposals": payload,
            }))
            .expect("serialize inbox")
        );
        return;
    }

    println!();
    println!(
        "  {}",
        format!(
            "VELA · INBOX · {}  ({} pending shown)",
            path.display(),
            pending.len()
        )
        .to_uppercase()
        .dimmed()
    );
    println!("  {}", style::tick_row(60));
    if pending.is_empty() {
        println!("  (inbox clean)");
        return;
    }
    for p in &pending {
        let assertion_text = p
            .payload
            .get("finding")
            .and_then(|f| f.get("assertion"))
            .and_then(|a| a.get("text"))
            .and_then(|t| t.as_str())
            .unwrap_or("");
        let assertion_type = p
            .payload
            .get("finding")
            .and_then(|f| f.get("assertion"))
            .and_then(|a| a.get("type"))
            .and_then(|t| t.as_str())
            .unwrap_or("");
        let composite = score_map
            .get(&p.id)
            .map(|(pl, e, s, d)| 0.4 * pl + 0.3 * e + 0.2 * s - 0.3 * d);
        let score_str = composite
            .map(|c| format!("[{:.2}]", c))
            .unwrap_or_else(|| "[—]   ".to_string());
        let kind_short = if p.kind.len() > 12 {
            format!("{}…", &p.kind[..11])
        } else {
            p.kind.clone()
        };
        let summary: String = if !assertion_text.is_empty() {
            assertion_text.chars().take(80).collect()
        } else {
            p.reason.chars().take(80).collect()
        };
        println!(
            "  {}  {}  {:<13}  {:<18}  {}",
            score_str, p.id, kind_short, assertion_type, summary
        );
    }
    println!();
}

/// v0.42: Conversational substrate access. Thin REPL over kernel
/// queries. Doesn't pretend to be an agent — every answer comes from
/// a structured query the kernel can produce deterministically. The
/// goal is fluency, not magic.
fn cmd_ask(path: &Path, question: &str, json: bool) {
    let project = repo::load_from_path(path).unwrap_or_else(|e| fail_return(&e));

    if question.trim().is_empty() {
        // REPL mode.
        use std::io::{BufRead, Write};
        println!();
        println!(
            "  {}",
            format!("VELA · ASK · {}", path.display())
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        println!("  Ask a question. Type `exit` to quit.");
        println!("  Examples:");
        println!("    · what's pending?");
        println!("    · what's underidentified?");
        println!("    · how many findings?");
        println!("    · what changed recently?");
        println!("    · who has what calibration?");
        println!();
        let stdin = std::io::stdin();
        let mut stdout = std::io::stdout();
        loop {
            print!("  ask> ");
            stdout.flush().ok();
            let mut line = String::new();
            if stdin.lock().read_line(&mut line).is_err() {
                break;
            }
            let q = line.trim();
            if q.is_empty() {
                continue;
            }
            if matches!(q, "exit" | "quit" | "q") {
                break;
            }
            answer(&project, q, false);
        }
        return;
    }

    answer(&project, question, json);
}

fn answer(project: &crate::project::Project, q: &str, json: bool) {
    let lower = q.to_lowercase();

    // Pattern: pending / inbox.
    if lower.contains("pending")
        || lower.contains("inbox")
        || lower.contains("queue")
        || lower.contains("to review")
    {
        let pending: Vec<&crate::proposals::StateProposal> = project
            .proposals
            .iter()
            .filter(|p| p.status == "pending_review")
            .collect();
        let mut by_kind: std::collections::BTreeMap<String, usize> = Default::default();
        for p in &pending {
            *by_kind.entry(p.kind.clone()).or_insert(0) += 1;
        }
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "answer": "pending",
                    "total": pending.len(),
                    "by_kind": by_kind,
                }))
                .unwrap()
            );
        } else {
            println!("  {} pending proposals.", pending.len());
            for (k, n) in &by_kind {
                println!("    · {n:>3}  {k}");
            }
            if pending.is_empty() {
                println!("  Inbox is clean.");
            } else {
                println!("  Run `vela inbox <frontier>` to triage.");
            }
        }
        return;
    }

    // Pattern: underidentified / conditional / audit.
    if lower.contains("underident")
        || lower.contains("audit")
        || lower.contains("identif")
        || lower.contains("causal")
    {
        let entries = crate::causal_reasoning::audit_frontier(project);
        let summary = crate::causal_reasoning::summarize_audit(&entries);
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "answer": "audit",
                    "summary": {
                        "identified": summary.identified,
                        "conditional": summary.conditional,
                        "underidentified": summary.underidentified,
                        "underdetermined": summary.underdetermined,
                    },
                }))
                .unwrap()
            );
        } else {
            println!(
                "  Causal audit: {} identified · {} conditional · {} underidentified · {} underdetermined.",
                summary.identified,
                summary.conditional,
                summary.underidentified,
                summary.underdetermined,
            );
            if summary.underidentified > 0 {
                println!(
                    "  The {} underidentified findings are concrete review items:",
                    summary.underidentified
                );
                for e in entries
                    .iter()
                    .filter(|e| {
                        matches!(
                            e.verdict,
                            crate::causal_reasoning::Identifiability::Underidentified
                        )
                    })
                    .take(8)
                {
                    let txt: String = e.assertion_text.chars().take(70).collect();
                    println!("    · {}  {}", e.finding_id, txt);
                }
            }
        }
        return;
    }

    // Pattern: recent / changed / log.
    if lower.contains("recent")
        || lower.contains("changed")
        || lower.contains("latest")
        || lower.contains("happen")
    {
        let mut events: Vec<&crate::events::StateEvent> = project.events.iter().collect();
        events.sort_by(|a, b| b.timestamp.cmp(&a.timestamp));
        events.truncate(8);
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "answer": "recent_events",
                    "events": events.iter().map(|e| json!({
                        "id": e.id, "kind": e.kind, "timestamp": e.timestamp,
                        "actor": e.actor.id, "target": e.target.id,
                    })).collect::<Vec<_>>(),
                }))
                .unwrap()
            );
        } else {
            println!("  Most recent {} events:", events.len());
            for e in &events {
                let when = fmt_timestamp(&e.timestamp);
                println!("    · {when}  {:<28}  {}", e.kind, e.target.id);
            }
        }
        return;
    }

    // Pattern: how many / count.
    if lower.starts_with("how many") || lower.contains("count") || lower.contains("total") {
        let n = project.findings.len();
        let evs = project.events.len();
        let peers = project.peers.len();
        let actors = project.actors.len();
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "answer": "counts",
                    "findings": n,
                    "events": evs,
                    "peers": peers,
                    "actors": actors,
                    "replications": project.replications.len(),
                    "predictions": project.predictions.len(),
                }))
                .unwrap()
            );
        } else {
            println!("  {n} findings · {evs} events · {actors} actors · {peers} peers.");
            println!(
                "  {} replications · {} predictions · {} datasets · {} code artifacts.",
                project.replications.len(),
                project.predictions.len(),
                project.datasets.len(),
                project.code_artifacts.len(),
            );
        }
        return;
    }

    // Pattern: calibration.
    if lower.contains("calibration") || lower.contains("brier") || lower.contains("predict") {
        let records =
            crate::calibration::calibration_records(&project.predictions, &project.resolutions);
        if json {
            println!("{}", serde_json::to_string_pretty(&records).unwrap());
        } else if records.is_empty() {
            println!("  No predictions yet. The calibration ledger is empty.");
        } else {
            println!("  Calibration over {} actor(s):", records.len());
            for r in &records {
                let brier = r
                    .brier_score
                    .map(|b| format!("{:.3}", b))
                    .unwrap_or_else(|| "—".into());
                println!(
                    "    · {:<28}  predictions {} · resolved {} · expired {} · Brier {}",
                    r.actor, r.n_predictions, r.n_resolved, r.n_expired, brier
                );
            }
        }
        return;
    }

    // Pattern: federation / peers / sync.
    if lower.contains("peer")
        || lower.contains("federat")
        || lower.contains("sync")
        || lower.contains("conflict")
    {
        let mut total_conflicts = 0usize;
        for e in &project.events {
            if e.kind == "frontier.conflict_detected" {
                total_conflicts += 1;
            }
        }
        if json {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "answer": "federation",
                    "peers": project.peers.iter().map(|p| &p.id).collect::<Vec<_>>(),
                    "total_conflicts": total_conflicts,
                }))
                .unwrap()
            );
        } else {
            println!("  {} peer(s) registered:", project.peers.len());
            for p in &project.peers {
                println!("    · {:<24}  {}", p.id, p.url);
            }
            println!("  {total_conflicts} conflict events on the canonical log.");
        }
        return;
    }

    // Fallback.
    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "answer": "unknown_question",
                "question": q,
                "hint": "Try: pending, audit, recent, how many, calibration, peers."
            }))
            .unwrap()
        );
    } else {
        println!("  Don't know how to route that question yet.");
        println!("  Try: pending · audit · recent · how many · calibration · peers");
    }
}

fn frontier_label(p: &crate::project::Project) -> String {
    if p.project.name.trim().is_empty() {
        "(unnamed)".to_string()
    } else {
        p.project.name.clone()
    }
}

fn fmt_timestamp(ts: &str) -> String {
    // RFC 3339 → "MM-DD HH:MM" for human reading. Falls back to first
    // 16 chars if parsing fails (which is enough to be readable).
    chrono::DateTime::parse_from_rfc3339(ts)
        .map(|dt| dt.format("%m-%d %H:%M").to_string())
        .unwrap_or_else(|_| ts.chars().take(16).collect())
}

fn cmd_stats(path: &Path) {
    let frontier = load_frontier_or_fail(path);
    let s = &frontier.stats;
    println!();
    println!("  {}", "FRONTIER · V0.36.0".dimmed());
    println!("  {}", frontier.project.name.bold());
    println!("  {}", style::tick_row(60));
    println!("  id:             {}", frontier.frontier_id());
    println!("  compiled:       {}", frontier.project.compiled_at);
    println!("  papers:         {}", frontier.project.papers_processed);
    println!("  findings:       {}", s.findings);
    println!("  links:          {}", s.links);
    println!("  replicated:     {}", s.replicated);
    println!("  avg confidence: {}", s.avg_confidence);
    println!("  gaps:           {}", s.gaps);
    println!("  contested:      {}", s.contested);
    println!("  reviewed:       {}", s.human_reviewed);
    println!("  proposals:      {}", s.proposal_count);
    println!(
        "  recorded proof: {}",
        frontier.proof_state.latest_packet.status
    );
    if frontier.proof_state.latest_packet.status != "never_exported" {
        println!(
            "  proof note:     recorded frontier metadata; packet files are checked by `vela packet validate`"
        );
    }
    if !s.categories.is_empty() {
        println!();
        println!("  {}", "categories".dimmed());
        let mut categories = s.categories.iter().collect::<Vec<_>>();
        categories.sort_by(|a, b| b.1.cmp(a.1));
        for (category, count) in categories {
            println!("    {category}: {}", count);
        }
    }
    println!();
    println!("  {}", style::tick_row(60));
    println!();
}

fn cmd_proposals(action: ProposalAction) {
    match action {
        ProposalAction::List {
            frontier,
            status,
            json,
        } => {
            let frontier_state =
                repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let proposals_list = proposals::list(&frontier_state, status.as_deref());
            let payload = json!({
                "ok": true,
                "command": "proposals.list",
                "frontier": frontier_state.project.name,
                "status_filter": status,
                "summary": proposals::summary(&frontier_state),
                "proposals": proposals_list,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize proposals list")
                );
            } else {
                println!("vela proposals list");
                println!("  frontier: {}", frontier_state.project.name);
                println!(
                    "  proposals: {}",
                    payload["proposals"].as_array().map_or(0, Vec::len)
                );
            }
        }
        ProposalAction::Show {
            frontier,
            proposal_id,
            json,
        } => {
            let frontier_state =
                repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let proposal =
                proposals::show(&frontier_state, &proposal_id).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "proposals.show",
                "frontier": frontier_state.project.name,
                "proposal": proposal,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize proposal show")
                );
            } else {
                println!("vela proposals show");
                println!("  frontier: {}", frontier_state.project.name);
                println!("  proposal: {}", proposal_id);
                println!("  kind: {}", proposal.kind);
                println!("  status: {}", proposal.status);
            }
        }
        ProposalAction::Preview {
            frontier,
            proposal_id,
            reviewer,
            json,
        } => {
            let preview = proposals::preview_at_path(&frontier, &proposal_id, &reviewer)
                .unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "proposals.preview",
                "frontier": frontier.display().to_string(),
                "preview": preview,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize proposal preview")
                );
            } else {
                println!("vela proposals preview");
                println!("  proposal: {}", proposal_id);
                println!("  kind: {}", preview.kind);
                println!(
                    "  findings: {} -> {}",
                    preview.findings_before, preview.findings_after
                );
                println!(
                    "  artifacts: {} -> {}",
                    preview.artifacts_before, preview.artifacts_after
                );
                println!(
                    "  events: {} -> {}",
                    preview.events_before, preview.events_after
                );
                if !preview.changed_findings.is_empty() {
                    println!(
                        "  findings changed: {}",
                        preview.changed_findings.join(", ")
                    );
                }
                if !preview.changed_artifacts.is_empty() {
                    println!(
                        "  artifacts changed: {}",
                        preview.changed_artifacts.join(", ")
                    );
                }
                if !preview.event_kinds.is_empty() {
                    println!("  event kinds: {}", preview.event_kinds.join(", "));
                }
                println!("  event: {}", preview.applied_event_id);
            }
        }
        ProposalAction::Import {
            frontier,
            source,
            json,
        } => {
            let report =
                proposals::import_from_path(&frontier, &source).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "proposals.import",
                "frontier": frontier.display().to_string(),
                "source": source.display().to_string(),
                "summary": {
                    "imported": report.imported,
                    "applied": report.applied,
                    "rejected": report.rejected,
                    "duplicates": report.duplicates,
                },
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize proposal import")
                );
            } else {
                println!(
                    "Imported {} proposals into {}",
                    report.imported, report.wrote_to
                );
            }
        }
        ProposalAction::Validate { source, json } => {
            let report = proposals::validate_source(&source).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": report.ok,
                "command": "proposals.validate",
                "source": source.display().to_string(),
                "summary": {
                    "checked": report.checked,
                    "valid": report.valid,
                    "invalid": report.invalid,
                },
                "proposal_ids": report.proposal_ids,
                "errors": report.errors,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize proposal validation")
                );
            } else if report.ok {
                println!("{} validated {} proposals", style::ok("ok"), report.valid);
            } else {
                println!(
                    "{} validated {} proposals, {} invalid",
                    style::lost("lost"),
                    report.valid,
                    report.invalid
                );
                for error in &report.errors {
                    println!("  · {error}");
                }
                std::process::exit(1);
            }
        }
        ProposalAction::Export {
            frontier,
            output,
            status,
            json,
        } => {
            let count = proposals::export_to_path(&frontier, &output, status.as_deref())
                .unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "proposals.export",
                "frontier": frontier.display().to_string(),
                "output": output.display().to_string(),
                "status": status,
                "exported": count,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize proposal export")
                );
            } else {
                println!("sealed · {count} proposals · {}", output.display());
            }
        }
        ProposalAction::Accept {
            frontier,
            proposal_id,
            reviewer,
            reason,
            json,
        } => {
            let event_id = proposals::accept_at_path(&frontier, &proposal_id, &reviewer, &reason)
                .unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "proposals.accept",
                "frontier": frontier.display().to_string(),
                "proposal_id": proposal_id,
                "reviewer": reviewer,
                "applied_event_id": event_id,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize proposal accept")
                );
            } else {
                println!(
                    "{} accepted and applied proposal {}",
                    style::ok("ok"),
                    proposal_id
                );
                println!("  event: {}", event_id);
            }
        }
        ProposalAction::Reject {
            frontier,
            proposal_id,
            reviewer,
            reason,
            json,
        } => {
            proposals::reject_at_path(&frontier, &proposal_id, &reviewer, &reason)
                .unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "proposals.reject",
                "frontier": frontier.display().to_string(),
                "proposal_id": proposal_id,
                "reviewer": reviewer,
                "status": "rejected",
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize proposal reject")
                );
            } else {
                println!(
                    "{} rejected proposal {}",
                    style::warn("rejected"),
                    proposal_id
                );
            }
        }
    }
}

fn cmd_artifact_to_state(
    frontier: &Path,
    packet: &Path,
    actor: &str,
    apply_artifacts: bool,
    json: bool,
) {
    let report =
        crate::artifact_to_state::import_packet_at_path(frontier, packet, actor, apply_artifacts)
            .unwrap_or_else(|e| fail_return(&e));
    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&report)
                .expect("failed to serialize artifact-to-state report")
        );
    } else {
        println!("vela artifact-to-state");
        println!("  packet: {}", report.packet_id);
        println!("  frontier: {}", report.frontier);
        println!("  artifact proposals: {}", report.artifact_proposals);
        println!("  finding proposals: {}", report.finding_proposals);
        println!("  gap proposals: {}", report.gap_proposals);
        println!(
            "  applied artifact events: {}",
            report.applied_artifact_events
        );
        println!(
            "  pending truth proposals: {}",
            report.pending_truth_proposals
        );
    }
}

async fn cmd_bridge_kit(action: BridgeKitAction) {
    match action {
        BridgeKitAction::Validate { source, json } => {
            let report = crate::artifact_to_state::validate_bridge_kit_path(&source);
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&report)
                        .expect("failed to serialize bridge-kit validation report")
                );
            } else {
                println!("vela bridge-kit validate");
                println!("  source: {}", report.source);
                println!("  packets: {}", report.packet_count);
                println!("  valid: {}", report.valid_packet_count);
                println!("  invalid: {}", report.invalid_packet_count);
                for packet in &report.packets {
                    if packet.ok {
                        println!(
                            "  ok: {} · {} artifacts · {} claims · {} needs",
                            packet
                                .packet_id
                                .as_deref()
                                .unwrap_or("packet id unavailable"),
                            packet.artifact_count,
                            packet.candidate_claim_count,
                            packet.open_need_count
                        );
                    } else {
                        println!("  invalid: {} · {}", packet.path, packet.errors.join("; "));
                    }
                }
                for error in &report.errors {
                    println!("  error: {error}");
                }
            }
            if !report.ok {
                std::process::exit(1);
            }
        }
        BridgeKitAction::VerifyProvenance { packet, json } => {
            let report = verify_packet_provenance(&packet).await;
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&report)
                        .expect("failed to serialize provenance verification report")
                );
            } else {
                println!("vela bridge-kit verify-provenance");
                println!("  packet: {}", report.packet);
                println!("  identifiers: {}", report.identifiers.len());
                println!("  resolved: {}", report.resolved_count);
                println!("  unresolved: {}", report.unresolved_count);
                println!("  skipped: {}", report.skipped_count);
                for entry in &report.identifiers {
                    let status = match entry.status.as_str() {
                        "resolved" => "ok ",
                        "unresolved" => "FAIL",
                        "skipped" => "skip",
                        _ => "?   ",
                    };
                    println!(
                        "  {} {} ({})",
                        status,
                        entry.identifier,
                        entry.note.as_deref().unwrap_or(entry.kind.as_str())
                    );
                }
            }
            if report.unresolved_count > 0 {
                std::process::exit(1);
            }
        }
    }
}

#[derive(Debug, Clone, Serialize)]
struct ProvenanceVerificationReport {
    command: String,
    packet: String,
    identifiers: Vec<ProvenanceVerificationEntry>,
    resolved_count: usize,
    unresolved_count: usize,
    skipped_count: usize,
}

#[derive(Debug, Clone, Serialize)]
struct ProvenanceVerificationEntry {
    identifier: String,
    kind: String,
    status: String,
    #[serde(skip_serializing_if = "Option::is_none")]
    note: Option<String>,
}

/// v0.108.3: walk a packet's artifacts and candidate-claim
/// source_refs, extract recognized DOI/PMID identifiers, ask
/// the upstream registry whether each one resolves. Closes
/// part of THREAT_MODEL.md A6 (citation poisoning).
async fn verify_packet_provenance(packet_path: &Path) -> ProvenanceVerificationReport {
    use crate::artifact_to_state::ArtifactPacket;
    let raw = std::fs::read_to_string(packet_path)
        .unwrap_or_else(|e| fail_return(&format!("read packet: {e}")));
    let parsed: ArtifactPacket =
        serde_json::from_str(&raw).unwrap_or_else(|e| fail_return(&format!("parse packet: {e}")));
    let packet = parsed
        .validate()
        .unwrap_or_else(|e| fail_return(&format!("validate packet: {e}")));

    // Collect candidate identifiers from every locator and source_ref.
    let mut candidates: std::collections::BTreeSet<String> = std::collections::BTreeSet::new();
    for artifact in &packet.artifacts {
        if let Some(ident) = extract_identifier(&artifact.locator) {
            candidates.insert(ident);
        }
    }
    for claim in &packet.candidate_claims {
        for source_ref in &claim.source_refs {
            if let Some(ident) = extract_identifier(source_ref) {
                candidates.insert(ident);
            }
        }
    }

    let client = reqwest::Client::builder()
        .user_agent("vela/0.108 (+https://github.com/vela-science/vela)")
        .timeout(std::time::Duration::from_secs(15))
        .build()
        .unwrap_or_else(|e| fail_return(&format!("build http client: {e}")));

    let mut entries: Vec<ProvenanceVerificationEntry> = Vec::new();
    let mut resolved = 0usize;
    let mut unresolved = 0usize;
    let mut skipped = 0usize;
    for candidate in &candidates {
        let entry = if let Some(doi) = candidate.strip_prefix("doi:") {
            verify_doi(&client, doi).await
        } else if let Some(pmid) = candidate.strip_prefix("pmid:") {
            verify_pmid(&client, pmid).await
        } else {
            ProvenanceVerificationEntry {
                identifier: candidate.clone(),
                kind: "unknown".to_string(),
                status: "skipped".to_string(),
                note: Some("no recognized identifier prefix".to_string()),
            }
        };
        match entry.status.as_str() {
            "resolved" => resolved += 1,
            "unresolved" => unresolved += 1,
            _ => skipped += 1,
        }
        entries.push(entry);
    }

    ProvenanceVerificationReport {
        command: "bridge-kit.verify-provenance".to_string(),
        packet: packet_path.display().to_string(),
        identifiers: entries,
        resolved_count: resolved,
        unresolved_count: unresolved,
        skipped_count: skipped,
    }
}

/// Extract a recognizable identifier from an artifact locator or
/// candidate-claim source_ref. Returns canonical `doi:<doi>` or
/// `pmid:<pmid>` form, or None when the string carries no
/// resolvable identifier.
fn extract_identifier(s: &str) -> Option<String> {
    let trimmed = s.trim();
    if trimmed.is_empty() {
        return None;
    }
    // Already prefixed.
    if trimmed.starts_with("doi:") || trimmed.starts_with("pmid:") {
        return Some(trimmed.to_string());
    }
    // doi.org / dx.doi.org URL forms.
    for prefix in ["https://doi.org/", "http://doi.org/", "https://dx.doi.org/"] {
        if let Some(rest) = trimmed.strip_prefix(prefix) {
            return Some(format!("doi:{rest}"));
        }
    }
    // PubMed URL forms.
    for prefix in [
        "https://pubmed.ncbi.nlm.nih.gov/",
        "http://pubmed.ncbi.nlm.nih.gov/",
    ] {
        if let Some(rest) = trimmed.strip_prefix(prefix) {
            let pmid = rest.trim_end_matches('/');
            return Some(format!("pmid:{pmid}"));
        }
    }
    // Bare DOI shape: "10.<numbers>/<rest>".
    if trimmed.starts_with("10.") && trimmed.contains('/') && !trimmed.contains(' ') {
        return Some(format!("doi:{trimmed}"));
    }
    None
}

async fn verify_doi(client: &reqwest::Client, doi: &str) -> ProvenanceVerificationEntry {
    let url = format!("https://api.crossref.org/works/{doi}");
    match client.get(&url).send().await {
        Ok(resp) if resp.status().is_success() => ProvenanceVerificationEntry {
            identifier: format!("doi:{doi}"),
            kind: "doi".to_string(),
            status: "resolved".to_string(),
            note: None,
        },
        Ok(resp) => ProvenanceVerificationEntry {
            identifier: format!("doi:{doi}"),
            kind: "doi".to_string(),
            status: "unresolved".to_string(),
            note: Some(format!("crossref returned {}", resp.status())),
        },
        Err(e) => ProvenanceVerificationEntry {
            identifier: format!("doi:{doi}"),
            kind: "doi".to_string(),
            status: "skipped".to_string(),
            note: Some(format!("crossref unreachable: {e}")),
        },
    }
}

async fn verify_pmid(client: &reqwest::Client, pmid: &str) -> ProvenanceVerificationEntry {
    let url = format!(
        "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id={pmid}&retmode=json"
    );
    match client.get(&url).send().await {
        Ok(resp) if resp.status().is_success() => {
            // PubMed esummary returns 200 even for nonexistent ids;
            // we have to inspect the result body for the id key.
            let body: serde_json::Value = resp.json().await.unwrap_or(serde_json::Value::Null);
            let result = body.get("result");
            let uids = result
                .and_then(|r| r.get("uids"))
                .and_then(|u| u.as_array());
            let resolved = uids.is_some_and(|a| !a.is_empty());
            if resolved {
                ProvenanceVerificationEntry {
                    identifier: format!("pmid:{pmid}"),
                    kind: "pmid".to_string(),
                    status: "resolved".to_string(),
                    note: None,
                }
            } else {
                ProvenanceVerificationEntry {
                    identifier: format!("pmid:{pmid}"),
                    kind: "pmid".to_string(),
                    status: "unresolved".to_string(),
                    note: Some("eutils returned empty uids".to_string()),
                }
            }
        }
        Ok(resp) => ProvenanceVerificationEntry {
            identifier: format!("pmid:{pmid}"),
            kind: "pmid".to_string(),
            status: "unresolved".to_string(),
            note: Some(format!("eutils returned {}", resp.status())),
        },
        Err(e) => ProvenanceVerificationEntry {
            identifier: format!("pmid:{pmid}"),
            kind: "pmid".to_string(),
            status: "skipped".to_string(),
            note: Some(format!("eutils unreachable: {e}")),
        },
    }
}

async fn cmd_source_adapter(action: SourceAdapterAction) {
    match action {
        SourceAdapterAction::Run {
            frontier,
            adapter,
            actor,
            entries,
            priority,
            include_excluded,
            allow_partial,
            dry_run,
            input_dir,
            apply_artifacts,
            json,
        } => {
            let report = crate::source_adapters::run(
                &frontier,
                crate::source_adapters::SourceAdapterRunOptions {
                    adapter,
                    actor,
                    entries,
                    priority,
                    include_excluded,
                    allow_partial,
                    dry_run,
                    input_dir,
                    apply_artifacts,
                },
            )
            .await
            .unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&report)
                        .expect("failed to serialize source adapter report")
                );
            } else {
                println!("vela source-adapter run");
                println!("  adapter: {}", report.adapter);
                println!("  run: {}", report.run_id);
                println!("  frontier: {}", report.frontier);
                println!("  selected entries: {}", report.selected_entries);
                println!("  fetched records: {}", report.fetched_records);
                println!("  changed records: {}", report.changed_records);
                println!("  unchanged records: {}", report.unchanged_records);
                println!("  failed records: {}", report.failed_records.len());
                if let Some(packet_id) = report.packet_id {
                    println!("  packet: {packet_id}");
                }
                println!("  artifact proposals: {}", report.artifact_proposals);
                println!("  review note proposals: {}", report.review_note_proposals);
                println!("  applied events: {}", report.applied_event_ids.len());
            }
        }
    }
}

fn cmd_runtime_adapter(action: RuntimeAdapterAction) {
    match action {
        RuntimeAdapterAction::Run {
            frontier,
            adapter,
            input,
            actor,
            dry_run,
            apply_artifacts,
            json,
        } => {
            let report = crate::runtime_adapters::run(
                &frontier,
                crate::runtime_adapters::RuntimeAdapterRunOptions {
                    adapter,
                    input,
                    actor,
                    dry_run,
                    apply_artifacts,
                },
            )
            .unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&report)
                        .expect("failed to serialize runtime adapter report")
                );
            } else {
                println!("vela runtime-adapter run");
                println!("  adapter: {}", report.adapter);
                println!("  run: {}", report.run_id);
                println!("  frontier: {}", report.frontier);
                if let Some(packet_id) = report.packet_id {
                    println!("  packet: {packet_id}");
                }
                println!("  artifact proposals: {}", report.artifact_proposals);
                println!("  finding proposals: {}", report.finding_proposals);
                println!("  gap proposals: {}", report.gap_proposals);
                println!("  review note proposals: {}", report.review_note_proposals);
                println!(
                    "  applied artifact events: {}",
                    report.applied_artifact_events
                );
                println!(
                    "  pending truth proposals: {}",
                    report.pending_truth_proposals
                );
            }
        }
    }
}

fn cmd_sign(action: SignAction) {
    match action {
        SignAction::GenerateKeypair { out, json } => {
            let public_key = sign::generate_keypair(&out).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "sign.generate-keypair",
                "output_dir": out.display().to_string(),
                "public_key": public_key,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize sign.generate-keypair")
                );
            } else {
                println!("{} keypair · {}", style::ok("generated"), out.display());
                println!("  public key: {public_key}");
            }
        }
        SignAction::Apply {
            frontier,
            private_key,
            json,
        } => {
            let count =
                sign::sign_frontier(&frontier, &private_key).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "sign.apply",
                "frontier": frontier.display().to_string(),
                "private_key": private_key.display().to_string(),
                "signed": count,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload).expect("failed to serialize sign.apply")
                );
            } else {
                println!(
                    "{} {count} findings in {}",
                    style::ok("signed"),
                    frontier.display()
                );
            }
        }
        SignAction::Verify {
            frontier,
            public_key,
            json,
        } => {
            let report = sign::verify_frontier(&frontier, public_key.as_deref())
                .unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&report).expect("failed to serialize sign.verify")
                );
            } else {
                println!();
                println!(
                    "  {}",
                    format!("VELA · SIGN · VERIFY · {}", frontier.display())
                        .to_uppercase()
                        .dimmed()
                );
                println!("  {}", style::tick_row(60));
                println!("  total findings:   {}", report.total_findings);
                println!("  signed:           {}", report.signed);
                println!("  unsigned:         {}", report.unsigned);
                println!("  valid:            {}", report.valid);
                println!("  invalid:          {}", report.invalid);
                if report.findings_with_threshold > 0 {
                    println!("  with threshold:   {}", report.findings_with_threshold);
                    println!("  jointly accepted: {}", report.jointly_accepted);
                }
            }
        }
        SignAction::ThresholdSet {
            frontier,
            finding_id,
            to,
            json,
        } => {
            if to == 0 {
                fail("--to must be >= 1");
            }
            let mut project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let Some(idx) = project.findings.iter().position(|f| f.id == finding_id) else {
                fail(&format!("finding '{finding_id}' not present in frontier"));
            };
            project.findings[idx].flags.signature_threshold = Some(to);
            // Re-derive the joint-accept flag immediately; if the
            // existing signature pool already meets the threshold, the
            // finding becomes jointly_accepted on the same write.
            sign::refresh_jointly_accepted(&mut project);
            let met = project.findings[idx].flags.jointly_accepted;
            repo::save_to_path(&frontier, &project).unwrap_or_else(|e| fail_return(&e));

            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "sign.threshold-set",
                        "finding_id": finding_id,
                        "threshold": to,
                        "jointly_accepted": met,
                        "frontier": frontier.display().to_string(),
                    }))
                    .expect("failed to serialize sign.threshold-set")
                );
            } else {
                println!(
                    "{} signature_threshold={to} on {finding_id} ({})",
                    style::ok("set"),
                    if met {
                        "jointly accepted"
                    } else {
                        "awaiting signatures"
                    }
                );
            }
        }
    }
}

fn cmd_actor(action: ActorAction) {
    match action {
        ActorAction::Add {
            frontier,
            id,
            pubkey,
            tier,
            orcid,
            clearance,
            json,
        } => {
            // Validate the pubkey shape before mutating the frontier.
            let trimmed = pubkey.trim();
            if trimmed.len() != 64 || hex::decode(trimmed).is_err() {
                fail("Public key must be 64 hex characters (32-byte Ed25519 pubkey).");
            }
            // v0.43: Validate ORCID shape if supplied. Stored in bare form.
            let orcid_normalized = orcid
                .as_deref()
                .map(|s| sign::validate_orcid(s).unwrap_or_else(|e| fail_return(&e)));
            // v0.51: parse clearance up front so a typo fails at the
            // CLI boundary rather than silently degrading.
            let clearance: Option<crate::access_tier::AccessTier> = clearance.as_deref().map(|s| {
                crate::access_tier::AccessTier::parse(s).unwrap_or_else(|e| fail_return(&e))
            });

            let mut project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            if project.actors.iter().any(|actor| actor.id == id) {
                fail(&format!(
                    "Actor '{id}' already registered in this frontier."
                ));
            }
            project.actors.push(sign::ActorRecord {
                id: id.clone(),
                public_key: trimmed.to_string(),
                algorithm: "ed25519".to_string(),
                created_at: chrono::Utc::now().to_rfc3339(),
                tier: tier.clone(),
                orcid: orcid_normalized.clone(),
                access_clearance: clearance,
            });
            repo::save_to_path(&frontier, &project).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "actor.add",
                "frontier": frontier.display().to_string(),
                "actor_id": id,
                "public_key": trimmed,
                "tier": tier,
                "orcid": orcid_normalized,
                "registered_count": project.actors.len(),
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload).expect("failed to serialize actor.add")
                );
            } else {
                let tier_suffix = tier
                    .as_deref()
                    .map_or_else(String::new, |t| format!(" tier={t}"));
                println!(
                    "{} actor {} (pubkey {}{tier_suffix})",
                    style::ok("registered"),
                    id,
                    &trimmed[..16]
                );
            }
        }
        ActorAction::List { frontier, json } => {
            let project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            if json {
                let payload = json!({
                    "ok": true,
                    "command": "actor.list",
                    "frontier": frontier.display().to_string(),
                    "actors": project.actors,
                });
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload).expect("failed to serialize actor.list")
                );
            } else {
                println!();
                println!(
                    "  {}",
                    format!("VELA · ACTOR · LIST · {}", frontier.display())
                        .to_uppercase()
                        .dimmed()
                );
                println!("  {}", style::tick_row(60));
                if project.actors.is_empty() {
                    println!("  (no actors registered)");
                } else {
                    for actor in &project.actors {
                        println!(
                            "  {:<28} {}…  registered {}",
                            actor.id,
                            &actor.public_key[..16],
                            actor.created_at
                        );
                    }
                }
            }
        }
    }
}

/// v0.40: Causal-typing audit over a frontier.
fn cmd_causal(action: CausalAction) {
    use crate::causal_reasoning;

    match action {
        CausalAction::Audit {
            frontier,
            problems_only,
            json,
        } => {
            let project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let mut entries = causal_reasoning::audit_frontier(&project);
            if problems_only {
                entries.retain(|e| e.verdict.needs_reviewer_attention());
            }
            let summary = causal_reasoning::summarize_audit(&entries);

            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "causal.audit",
                        "frontier": frontier.display().to_string(),
                        "summary": summary,
                        "entries": entries,
                    }))
                    .expect("serialize causal.audit")
                );
                return;
            }

            println!();
            println!(
                "  {}",
                format!("VELA · CAUSAL · AUDIT · {}", frontier.display())
                    .to_uppercase()
                    .dimmed()
            );
            println!("  {}", style::tick_row(60));
            println!(
                "  total: {}  identified: {}  conditional: {}  underidentified: {}  underdetermined: {}",
                summary.total,
                summary.identified,
                summary.conditional,
                summary.underidentified,
                summary.underdetermined,
            );
            if entries.is_empty() {
                println!("  (no entries to report)");
                return;
            }
            for e in &entries {
                let chip = match e.verdict {
                    crate::causal_reasoning::Identifiability::Identified => style::ok("identified"),
                    crate::causal_reasoning::Identifiability::Conditional => {
                        style::warn("conditional")
                    }
                    crate::causal_reasoning::Identifiability::Underidentified => {
                        style::lost("underidentified")
                    }
                    crate::causal_reasoning::Identifiability::Underdetermined => {
                        style::warn("underdetermined")
                    }
                };
                let claim = e
                    .causal_claim
                    .map_or("none".to_string(), |c| format!("{c:?}").to_lowercase());
                let grade = e
                    .causal_evidence_grade
                    .map_or("none".to_string(), |g| format!("{g:?}").to_lowercase());
                println!();
                println!("  {chip}  {}  ({}/{})", e.finding_id, claim, grade);
                let assertion_short: String = e.assertion_text.chars().take(78).collect();
                println!("    {assertion_short}");
                println!("    {} {}", style::ok("why:"), e.rationale);
                if e.verdict.needs_reviewer_attention()
                    || matches!(
                        e.verdict,
                        crate::causal_reasoning::Identifiability::Underdetermined
                    )
                {
                    println!("    {} {}", style::ok("fix:"), e.remediation);
                }
            }
        }
        CausalAction::Effect {
            frontier,
            source,
            on: target,
            json,
        } => {
            use crate::causal_graph::{CausalEffectVerdict, identify_effect};

            let project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let verdict = identify_effect(&project, &source, &target);

            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "causal.effect",
                        "frontier": frontier.display().to_string(),
                        "source": source,
                        "target": target,
                        "verdict": verdict,
                    }))
                    .expect("serialize causal.effect")
                );
                return;
            }

            println!();
            println!(
                "  {}",
                format!("VELA · CAUSAL · EFFECT · {} → {}", source, target)
                    .to_uppercase()
                    .dimmed()
            );
            println!("  {}", style::tick_row(60));
            match verdict {
                CausalEffectVerdict::Identified {
                    adjustment_set,
                    back_door_paths_considered,
                } => {
                    if adjustment_set.is_empty() {
                        println!(
                            "  {}  no back-door adjustment needed",
                            style::ok("identified")
                        );
                    } else {
                        println!("  {}  identified by adjusting on:", style::ok("identified"));
                        for z in &adjustment_set {
                            println!("    · {z}");
                        }
                    }
                    println!(
                        "  back-door paths considered: {}",
                        back_door_paths_considered
                    );
                }
                CausalEffectVerdict::IdentifiedByFrontDoor { mediator_set } => {
                    println!(
                        "  {}  identified via front-door criterion (Pearl 1995 §3.3)",
                        style::ok("identified")
                    );
                    println!("  mediators that intercept all directed paths:");
                    for m in &mediator_set {
                        println!("    · {m}");
                    }
                    println!(
                        "  applies when source-target confounders are unobserved but the mediator chain is."
                    );
                }
                CausalEffectVerdict::NoCausalPath { reason } => {
                    println!("  {}  no causal path: {reason}", style::warn("no_path"));
                }
                CausalEffectVerdict::Underidentified {
                    unblocked_back_door_paths,
                    candidates_tried,
                } => {
                    println!(
                        "  {}  no observational adjustment set found ({} candidates tried)",
                        style::lost("underidentified"),
                        candidates_tried
                    );
                    println!("  open back-door paths:");
                    for path in unblocked_back_door_paths.iter().take(5) {
                        println!("    · {}", path.join(" — "));
                    }
                    println!(
                        "  remediation: either intervene experimentally on {source}, or extend the link graph to make a confounder observable."
                    );
                }
                CausalEffectVerdict::UnknownNode { which } => {
                    fail(&which);
                }
            }
            println!();
        }
        CausalAction::Graph {
            frontier,
            node,
            json,
        } => {
            use crate::causal_graph::CausalGraph;
            let project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let graph = CausalGraph::from_project(&project);

            // Build a serializable view: each node with its parents
            // and children. Optionally restrict to a single node.
            let nodes: Vec<&str> = if let Some(n) = node.as_deref() {
                if !graph.contains(n) {
                    fail(&format!("node not in frontier: {n}"));
                }
                vec![n]
            } else {
                project.findings.iter().map(|f| f.id.as_str()).collect()
            };

            if json {
                let payload: Vec<_> = nodes
                    .iter()
                    .map(|n| {
                        let parents: Vec<&str> = graph.parents_of(n).collect();
                        let children: Vec<&str> = graph.children_of(n).collect();
                        json!({
                            "node": n,
                            "parents": parents,
                            "children": children,
                        })
                    })
                    .collect();
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "causal.graph",
                        "node_count": graph.node_count(),
                        "edge_count": graph.edge_count(),
                        "nodes": payload,
                    }))
                    .expect("serialize causal.graph")
                );
                return;
            }

            println!();
            println!(
                "  {}",
                format!("VELA · CAUSAL · GRAPH · {}", frontier.display())
                    .to_uppercase()
                    .dimmed()
            );
            println!("  {}", style::tick_row(60));
            println!(
                "  {} nodes · {} edges",
                graph.node_count(),
                graph.edge_count()
            );
            println!();
            for n in &nodes {
                let parents: Vec<&str> = graph.parents_of(n).collect();
                let children: Vec<&str> = graph.children_of(n).collect();
                if parents.is_empty() && children.is_empty() && nodes.len() > 1 {
                    continue; // hide isolated nodes when listing all
                }
                println!("  {n}");
                if !parents.is_empty() {
                    println!("    parents:  {}", parents.join(", "));
                }
                if !children.is_empty() {
                    println!("    children: {}", children.join(", "));
                }
            }
        }
        CausalAction::Counterfactual {
            frontier,
            intervene_on,
            set_to,
            target,
            json,
        } => {
            use crate::counterfactual::{
                CounterfactualQuery, CounterfactualVerdict, answer_counterfactual,
            };

            let project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let query = CounterfactualQuery {
                intervene_on: intervene_on.clone(),
                set_to,
                target: target.clone(),
            };
            let verdict = answer_counterfactual(&project, &query);

            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "causal.counterfactual",
                        "frontier": frontier.display().to_string(),
                        "query": query,
                        "verdict": verdict,
                    }))
                    .expect("serialize causal.counterfactual")
                );
                return;
            }

            println!();
            println!(
                "  {}",
                format!(
                    "VELA · CAUSAL · COUNTERFACTUAL · do({intervene_on} := {set_to:.3}) → {target}"
                )
                .to_uppercase()
                .dimmed()
            );
            println!("  {}", style::tick_row(72));
            match verdict {
                CounterfactualVerdict::Resolved {
                    factual,
                    counterfactual,
                    delta,
                    paths_used,
                } => {
                    println!(
                        "  {}  factual: {factual:.3}  counterfactual: {counterfactual:.3}  delta: {delta:+.3}",
                        style::ok("resolved")
                    );
                    println!(
                        "  twin-network propagation through {} causal path(s):",
                        paths_used.len()
                    );
                    for p in paths_used.iter().take(5) {
                        println!("    · {}", p.join(" → "));
                    }
                    println!(
                        "  reading: \"if {intervene_on}'s confidence had been {set_to:.3} \
                        instead of factual, {target}'s confidence would shift by {delta:+.3}.\""
                    );
                }
                CounterfactualVerdict::MechanismUnspecified { unspecified_edges } => {
                    println!(
                        "  {}  causal path exists but {} edge(s) lack a mechanism annotation",
                        style::warn("mechanism_unspecified"),
                        unspecified_edges.len()
                    );
                    for (parent, child) in unspecified_edges.iter().take(8) {
                        println!("    · {parent} → {child}");
                    }
                    println!(
                        "  remediation: annotate one of the link mechanisms (linear / monotonic / threshold / saturating)."
                    );
                }
                CounterfactualVerdict::NoCausalPath { factual } => {
                    println!(
                        "  {}  no directed path from {intervene_on} to {target}; counterfactual = factual = {factual:.3}",
                        style::warn("no_path")
                    );
                }
                CounterfactualVerdict::UnknownNode { which } => {
                    fail(&format!("node not in frontier: {which}"));
                }
                CounterfactualVerdict::InvalidIntervention { reason } => {
                    fail(&reason);
                }
            }
            println!();
        }
    }
}

/// v0.46: Cross-frontier bridge runtime — derive, list, show,
/// confirm, and refute first-class `vbr_<id>` records.
fn cmd_bridges(action: BridgesAction) {
    use crate::bridge::{Bridge, BridgeStatus, derive_bridges};
    use std::collections::HashMap;

    fn bridges_dir(frontier: &Path) -> PathBuf {
        frontier.join(".vela/bridges")
    }

    fn load_bridge(frontier: &Path, id: &str) -> Result<Bridge, String> {
        let path = bridges_dir(frontier).join(format!("{id}.json"));
        if !path.is_file() {
            return Err(format!("bridge not found: {id}"));
        }
        let data = std::fs::read_to_string(&path).map_err(|e| format!("read {id}: {e}"))?;
        serde_json::from_str(&data).map_err(|e| format!("parse {id}: {e}"))
    }

    fn save_bridge(frontier: &Path, b: &Bridge) -> Result<(), String> {
        let dir = bridges_dir(frontier);
        std::fs::create_dir_all(&dir).map_err(|e| format!("mkdir bridges/: {e}"))?;
        let path = dir.join(format!("{}.json", b.id));
        let data = serde_json::to_string_pretty(b).map_err(|e| format!("serialize bridge: {e}"))?;
        std::fs::write(&path, format!("{data}\n")).map_err(|e| format!("write bridge: {e}"))
    }

    /// v0.67: shared default for the agent-driven write paths
    /// (bridge confirm/refute).
    fn default_reviewer_id() -> String {
        std::env::var("VELA_REVIEWER_ID").unwrap_or_else(|_| "reviewer:will-blair".to_string())
    }

    /// v0.67: emit a `bridge.reviewed` canonical event into the
    /// frontier's `.vela/events/` directory so federation sync can
    /// propagate the verdict. The bridge file mutation is the
    /// projection; this event is the authority.
    ///
    /// v0.73: tightens the spec gap surfaced in v0.72. Before
    /// emission, the function asks `validate_bridge_reviewed_against_state`
    /// to confirm the bridge is present on this frontier. The
    /// signature-pure validator already rejects bad payload shapes;
    /// this second pass rejects bridge_ids that don't exist locally.
    fn emit_bridge_reviewed_event(
        frontier: &Path,
        bridge_id: &str,
        status: &str,
        reviewer_id: &str,
        note: Option<&str>,
    ) -> Result<(), String> {
        let mut payload = serde_json::json!({
            "bridge_id": bridge_id,
            "status": status,
        });
        if let Some(n) = note
            && !n.trim().is_empty()
        {
            payload["note"] = serde_json::Value::String(n.to_string());
        }
        // v0.73: state-aware validation.
        let known_ids: Vec<String> = list_bridges(frontier)
            .unwrap_or_default()
            .into_iter()
            .map(|b| b.id)
            .collect();
        crate::events::validate_bridge_reviewed_against_state(&payload, &known_ids)?;
        let event = crate::events::new_bridge_reviewed_event(
            bridge_id,
            reviewer_id,
            "human",
            &format!("Bridge {status} by {reviewer_id}"),
            payload,
            Vec::new(),
        );
        let events_dir = frontier.join(".vela/events");
        std::fs::create_dir_all(&events_dir).map_err(|e| format!("mkdir .vela/events: {e}"))?;
        let event_path = events_dir.join(format!("{}.json", event.id));
        let data =
            serde_json::to_string_pretty(&event).map_err(|e| format!("serialize event: {e}"))?;
        std::fs::write(&event_path, format!("{data}\n")).map_err(|e| format!("write event: {e}"))
    }

    fn list_bridges(frontier: &Path) -> Result<Vec<Bridge>, String> {
        let dir = bridges_dir(frontier);
        if !dir.is_dir() {
            return Ok(Vec::new());
        }
        let mut out = Vec::new();
        for entry in std::fs::read_dir(&dir).map_err(|e| format!("read bridges/: {e}"))? {
            let entry = entry.map_err(|e| format!("read entry: {e}"))?;
            let path = entry.path();
            if path.extension().and_then(|s| s.to_str()) != Some("json") {
                continue;
            }
            let data = std::fs::read_to_string(&path).map_err(|e| format!("read {path:?}: {e}"))?;
            let b: Bridge =
                serde_json::from_str(&data).map_err(|e| format!("parse {path:?}: {e}"))?;
            out.push(b);
        }
        out.sort_by(|a, b| {
            b.finding_refs
                .len()
                .cmp(&a.finding_refs.len())
                .then(a.entity_name.cmp(&b.entity_name))
        });
        Ok(out)
    }

    match action {
        BridgesAction::Derive {
            frontier_a,
            label_a,
            frontier_b,
            label_b,
            json,
        } => {
            let a = repo::load_from_path(&frontier_a).unwrap_or_else(|e| fail_return(&e));
            let b = repo::load_from_path(&frontier_b).unwrap_or_else(|e| fail_return(&e));
            let now = chrono::Utc::now().to_rfc3339();
            let new_bridges =
                derive_bridges(&[(label_a.as_str(), &a), (label_b.as_str(), &b)], &now);

            // Merge: preserve status from existing bridges with the
            // same vbr_<id> (we don't blindly overwrite a Confirmed
            // bridge with a fresh Derived one).
            let existing = list_bridges(&frontier_a).unwrap_or_default();
            let existing_by_id: HashMap<String, Bridge> =
                existing.iter().map(|b| (b.id.clone(), b.clone())).collect();
            let mut written = 0;
            let mut preserved = 0;
            let mut new_ids = Vec::new();
            for mut bridge in new_bridges {
                if let Some(prev) = existing_by_id.get(&bridge.id)
                    && prev.status != BridgeStatus::Derived
                {
                    // Reviewer judgment is sticky.
                    bridge.status = prev.status;
                    bridge.derived_at = prev.derived_at.clone();
                    preserved += 1;
                }
                save_bridge(&frontier_a, &bridge).unwrap_or_else(|e| fail_return(&e));
                new_ids.push(bridge.id.clone());
                written += 1;
            }

            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "bridges.derive",
                        "frontier_a": frontier_a.display().to_string(),
                        "frontier_b": frontier_b.display().to_string(),
                        "bridges_written": written,
                        "reviewer_judgments_preserved": preserved,
                        "ids": new_ids,
                    }))
                    .expect("serialize bridges.derive")
                );
                return;
            }

            println!();
            println!(
                "  {}",
                format!("VELA · BRIDGES · DERIVE · {} ↔ {}", label_a, label_b)
                    .to_uppercase()
                    .dimmed()
            );
            println!("  {}", style::tick_row(60));
            println!("  {}  {} bridge(s) materialized", style::ok("ok"), written);
            if preserved > 0 {
                println!(
                    "  {}  {} reviewer judgment(s) preserved",
                    style::ok("kept"),
                    preserved
                );
            }
            for id in new_ids.iter().take(10) {
                println!("    · {id}");
            }
            if new_ids.len() > 10 {
                println!("    … and {} more", new_ids.len() - 10);
            }
            println!();
        }
        BridgesAction::List {
            frontier,
            status,
            json,
        } => {
            let mut bridges = list_bridges(&frontier).unwrap_or_else(|e| fail_return(&e));
            if let Some(s) = status.as_deref() {
                let want = match s.to_lowercase().as_str() {
                    "derived" => BridgeStatus::Derived,
                    "confirmed" => BridgeStatus::Confirmed,
                    "refuted" => BridgeStatus::Refuted,
                    other => fail_return(&format!(
                        "unknown bridge status '{other}' (try derived|confirmed|refuted)"
                    )),
                };
                bridges.retain(|b| b.status == want);
            }
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "bridges.list",
                        "frontier": frontier.display().to_string(),
                        "count": bridges.len(),
                        "bridges": bridges,
                    }))
                    .expect("serialize bridges.list")
                );
                return;
            }
            println!();
            println!(
                "  {}",
                format!("VELA · BRIDGES · LIST · {}", frontier.display())
                    .to_uppercase()
                    .dimmed()
            );
            println!("  {}", style::tick_row(60));
            println!("  {} bridge(s)", bridges.len());
            for b in &bridges {
                let chip = match b.status {
                    BridgeStatus::Derived => style::warn("derived"),
                    BridgeStatus::Confirmed => style::ok("confirmed"),
                    BridgeStatus::Refuted => style::lost("refuted"),
                };
                println!();
                println!(
                    "  {chip}  {}  {} ↔ findings:{}",
                    b.id,
                    b.entity_name,
                    b.finding_refs.len()
                );
                println!("    frontiers: {}", b.frontiers.join(", "));
                if let Some(t) = &b.tension {
                    println!("    tension:   {t}");
                }
            }
            println!();
        }
        BridgesAction::Show {
            frontier,
            bridge_id,
            json,
        } => {
            let b = load_bridge(&frontier, &bridge_id).unwrap_or_else(|e| fail_return(&e));
            if json {
                println!("{}", serde_json::to_string_pretty(&b).expect("serialize"));
                return;
            }
            println!();
            println!(
                "  {}",
                format!("VELA · BRIDGES · SHOW · {}", b.id)
                    .to_uppercase()
                    .dimmed()
            );
            println!("  {}", style::tick_row(60));
            println!("  entity:    {}", b.entity_name);
            println!("  status:    {:?}", b.status);
            println!("  frontiers: {}", b.frontiers.join(", "));
            if !b.frontier_ids.is_empty() {
                println!("  frontier_ids: {}", b.frontier_ids.join(", "));
            }
            if let Some(t) = &b.tension {
                println!("  tension:   {t}");
            }
            println!("  derived_at: {}", b.derived_at);
            println!("  finding refs ({}):", b.finding_refs.len());
            for r in &b.finding_refs {
                let dir = r.direction.as_deref().unwrap_or("—");
                let truncated: String = r.assertion_text.chars().take(72).collect();
                println!(
                    "    · [{}] {} (conf={:.2}, dir={})",
                    r.frontier, r.finding_id, r.confidence, dir
                );
                println!("      {truncated}");
            }
            println!();
        }
        BridgesAction::Confirm {
            frontier,
            bridge_id,
            reviewer,
            note,
            json,
        } => {
            let mut b = load_bridge(&frontier, &bridge_id).unwrap_or_else(|e| fail_return(&e));
            let reviewer_id = reviewer.unwrap_or_else(default_reviewer_id);
            b.status = BridgeStatus::Confirmed;
            save_bridge(&frontier, &b).unwrap_or_else(|e| fail_return(&e));
            // v0.67: emit canonical event so federation sync
            // propagates the verdict. The bridge file mutation above
            // is the projection; this event is the authority.
            let _ = emit_bridge_reviewed_event(
                &frontier,
                &bridge_id,
                "confirmed",
                &reviewer_id,
                note.as_deref(),
            );
            if json {
                println!("{}", serde_json::to_string_pretty(&b).expect("serialize"));
                return;
            }
            println!();
            println!("  {}  {} now confirmed", style::ok("confirmed"), b.id);
            println!();
        }
        BridgesAction::Refute {
            frontier,
            bridge_id,
            reviewer,
            note,
            json,
        } => {
            let mut b = load_bridge(&frontier, &bridge_id).unwrap_or_else(|e| fail_return(&e));
            let reviewer_id = reviewer.unwrap_or_else(default_reviewer_id);
            b.status = BridgeStatus::Refuted;
            save_bridge(&frontier, &b).unwrap_or_else(|e| fail_return(&e));
            let _ = emit_bridge_reviewed_event(
                &frontier,
                &bridge_id,
                "refuted",
                &reviewer_id,
                note.as_deref(),
            );
            if json {
                println!("{}", serde_json::to_string_pretty(&b).expect("serialize"));
                return;
            }
            println!();
            println!("  {}  {} now refuted", style::lost("refuted"), b.id);
            println!();
        }
    }
}

/// v0.39: Manage the federation peer registry.
fn cmd_federation(action: FederationAction) {
    use crate::federation::PeerHub;

    match action {
        FederationAction::PeerAdd {
            frontier,
            id,
            url,
            pubkey,
            note,
            json,
        } => {
            let peer = PeerHub {
                id: id.clone(),
                url: url.clone(),
                public_key: pubkey.trim().to_string(),
                added_at: chrono::Utc::now().to_rfc3339(),
                note: note.clone(),
            };
            peer.validate().unwrap_or_else(|e| fail_return(&e));

            let mut project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            if project.peers.iter().any(|p| p.id == id) {
                fail(&format!("peer '{id}' already in registry"));
            }
            project.peers.push(peer.clone());
            repo::save_to_path(&frontier, &project).unwrap_or_else(|e| fail_return(&e));

            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "federation.peer-add",
                        "frontier": frontier.display().to_string(),
                        "peer": peer,
                        "registered_count": project.peers.len(),
                    }))
                    .expect("serialize federation.peer-add")
                );
            } else {
                println!(
                    "{} peer {} (pubkey {}…) at {}",
                    style::ok("registered"),
                    id,
                    &peer.public_key[..16],
                    peer.url
                );
            }
        }
        FederationAction::PeerList { frontier, json } => {
            let project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "federation.peer-list",
                        "frontier": frontier.display().to_string(),
                        "peers": project.peers,
                    }))
                    .expect("serialize federation.peer-list")
                );
            } else {
                println!();
                println!(
                    "  {}",
                    format!("VELA · FEDERATION · PEERS · {}", frontier.display())
                        .to_uppercase()
                        .dimmed()
                );
                println!("  {}", style::tick_row(60));
                if project.peers.is_empty() {
                    println!("  (no peers registered)");
                } else {
                    for p in &project.peers {
                        let note_suffix = if p.note.is_empty() {
                            String::new()
                        } else {
                            format!("  · {}", p.note)
                        };
                        println!(
                            "  {:<24}  {}  {}…{note_suffix}",
                            p.id,
                            p.url,
                            &p.public_key[..16]
                        );
                    }
                }
            }
        }
        FederationAction::Sync {
            frontier,
            peer_id,
            url,
            via_hub,
            vfr_id,
            allow_cross_vfr,
            dry_run,
            json,
        } => {
            use crate::federation::{self, DiscoveryResult};

            let mut project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let Some(peer) = project.peers.iter().find(|p| p.id == peer_id).cloned() else {
                fail(&format!(
                    "peer '{peer_id}' not in registry; run `vela federation peer add` first"
                ));
            };
            let local_frontier_id = project.frontier_id();

            // v0.64: refuse cross-vfr sync without explicit opt-in.
            // The substrate path is honest about cross-vfr divergence
            // (every peer-side finding becomes a "missing_locally"
            // conflict), but in practice that floods the inbox with
            // noise. The intended use of `--via-hub --vfr-id` is to
            // sync against your OWN frontier_id on the peer hub.
            if via_hub
                && let Some(target) = vfr_id.as_deref()
                && target != local_frontier_id
                && !allow_cross_vfr
            {
                fail(&format!(
                    "cross-vfr sync refused: --vfr-id {target} differs from local frontier_id {local_frontier_id}. \
                     Pass --allow-cross-vfr to opt in (every peer-side finding will be recorded as a \
                     missing_locally conflict). Or omit --vfr-id to default to the local frontier id."
                ));
            }

            // v0.41.0: three sync modes (via-hub / direct-url / default-manifest-path).
            #[derive(Debug)]
            enum SyncOutcome {
                Resolved(crate::project::Project, String), // (peer state, source description)
                BrokenLocator(String, String, u16),        // (vfr_id, locator, status)
                UnverifiedEntry(String, String),           // (vfr_id, reason)
                EntryNotFound(String, u16),
            }

            let outcome = if via_hub {
                let target_vfr = vfr_id.clone().unwrap_or_else(|| local_frontier_id.clone());
                match federation::discover_peer_frontier(
                    &peer.url,
                    &target_vfr,
                    Some(&peer.public_key),
                ) {
                    DiscoveryResult::Resolved(p) => {
                        let src =
                            format!("{}/entries/{}", peer.url.trim_end_matches('/'), target_vfr);
                        SyncOutcome::Resolved(p, src)
                    }
                    DiscoveryResult::BrokenLocator {
                        vfr_id,
                        locator,
                        status,
                    } => SyncOutcome::BrokenLocator(vfr_id, locator, status),
                    DiscoveryResult::UnverifiedEntry { vfr_id, reason } => {
                        SyncOutcome::UnverifiedEntry(vfr_id, reason)
                    }
                    DiscoveryResult::EntryNotFound { vfr_id, status } => {
                        SyncOutcome::EntryNotFound(vfr_id, status)
                    }
                    DiscoveryResult::Unreachable { url, error } => {
                        fail(&format!("peer hub unreachable ({url}): {error}"));
                    }
                }
            } else {
                let resolved_url = url.unwrap_or_else(|| {
                    let base = peer.url.trim_end_matches('/');
                    format!("{base}/manifest/{local_frontier_id}.json")
                });
                match federation::fetch_peer_frontier(&resolved_url) {
                    Ok(p) => SyncOutcome::Resolved(p, resolved_url),
                    Err(e) => fail(&format!("direct fetch failed: {e}")),
                }
            };

            // Handle the non-resolved cases by emitting a single
            // synthetic conflict event and a sync record.
            let peer_source: String;
            let peer_state = match outcome {
                SyncOutcome::Resolved(p, src) => {
                    if !json {
                        println!("  · resolved via {src}");
                    }
                    peer_source = src;
                    p
                }
                SyncOutcome::BrokenLocator(vfr, locator, status) => {
                    if dry_run {
                        if json {
                            println!(
                                "{}",
                                serde_json::to_string_pretty(&json!({
                                    "ok": true,
                                    "command": "federation.sync",
                                    "dry_run": true,
                                    "outcome": "broken_locator",
                                    "vfr_id": vfr,
                                    "locator": locator,
                                    "http_status": status,
                                }))
                                .expect("serialize")
                            );
                        } else {
                            println!(
                                "{} dry-run: peer entry resolved but locator dead",
                                style::warn("broken_locator")
                            );
                            println!("  vfr_id:  {vfr}");
                            println!("  locator: {locator} (HTTP {status})");
                        }
                        return;
                    }
                    let report = federation::record_locator_failure(
                        &mut project,
                        &peer_id,
                        &vfr,
                        &locator,
                        status,
                    );
                    repo::save_to_path(&frontier, &project).unwrap_or_else(|e| fail_return(&e));
                    if json {
                        println!(
                            "{}",
                            serde_json::to_string_pretty(&json!({
                                "ok": true,
                                "command": "federation.sync",
                                "outcome": "broken_locator",
                                "report": report,
                            }))
                            .expect("serialize")
                        );
                    } else {
                        println!(
                            "{} sync recorded broken-locator conflict against {peer_id}",
                            style::warn("broken_locator")
                        );
                        println!("  vfr_id:  {vfr}");
                        println!("  locator: {locator} (HTTP {status})");
                        println!("  events appended: {}", report.events_appended);
                    }
                    return;
                }
                SyncOutcome::UnverifiedEntry(vfr, reason) => {
                    if dry_run {
                        if json {
                            println!(
                                "{}",
                                serde_json::to_string_pretty(&json!({
                                    "ok": true,
                                    "command": "federation.sync",
                                    "dry_run": true,
                                    "outcome": "unverified_peer_entry",
                                    "vfr_id": vfr,
                                    "reason": reason,
                                }))
                                .expect("serialize")
                            );
                        } else {
                            println!(
                                "{} dry-run: peer entry signature did not verify",
                                style::lost("unverified_peer_entry")
                            );
                            println!("  vfr_id: {vfr}");
                            println!("  reason: {reason}");
                        }
                        return;
                    }
                    let report =
                        federation::record_unverified_entry(&mut project, &peer_id, &vfr, &reason);
                    repo::save_to_path(&frontier, &project).unwrap_or_else(|e| fail_return(&e));
                    if json {
                        println!(
                            "{}",
                            serde_json::to_string_pretty(&json!({
                                "ok": true,
                                "command": "federation.sync",
                                "outcome": "unverified_peer_entry",
                                "report": report,
                            }))
                            .expect("serialize")
                        );
                    } else {
                        println!(
                            "{} sync halted; peer's registry entry signature did not verify",
                            style::lost("unverified_peer_entry")
                        );
                        println!("  vfr_id: {vfr}");
                        println!("  reason: {reason}");
                    }
                    return;
                }
                SyncOutcome::EntryNotFound(vfr, status) => {
                    if json {
                        println!(
                            "{}",
                            serde_json::to_string_pretty(&json!({
                                "ok": false,
                                "command": "federation.sync",
                                "outcome": "entry_not_found",
                                "vfr_id": vfr,
                                "http_status": status,
                            }))
                            .expect("serialize")
                        );
                    } else {
                        println!(
                            "{} peer's hub does not publish vfr_id {vfr} (HTTP {status})",
                            style::warn("entry_not_found")
                        );
                    }
                    return;
                }
            };

            if dry_run {
                let conflicts = federation::diff_frontiers(&project, &peer_state);
                if json {
                    println!(
                        "{}",
                        serde_json::to_string_pretty(&json!({
                            "ok": true,
                            "command": "federation.sync",
                            "dry_run": true,
                            "peer_id": peer_id,
                            "peer_source": peer_source,
                            "conflicts": conflicts,
                        }))
                        .expect("serialize federation.sync (dry-run)")
                    );
                } else {
                    println!(
                        "{} dry-run vs {peer_id} ({}): {} conflict(s)",
                        style::ok("ok"),
                        peer_source,
                        conflicts.len()
                    );
                    for c in &conflicts {
                        println!("  · {} {} {}", c.kind.as_str(), c.finding_id, c.detail);
                    }
                }
                return;
            }

            let report = federation::sync_with_peer(&mut project, &peer_id, &peer_state);
            repo::save_to_path(&frontier, &project).unwrap_or_else(|e| fail_return(&e));

            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "federation.sync",
                        "peer_id": peer_id,
                        "peer_source": peer_source,
                        "report": report,
                    }))
                    .expect("serialize federation.sync")
                );
            } else {
                println!(
                    "{} synced with {} ({})",
                    style::ok("ok"),
                    peer_id,
                    peer_source
                );
                println!(
                    "  our:    {}",
                    &report.our_snapshot_hash[..16.min(report.our_snapshot_hash.len())]
                );
                println!(
                    "  peer:   {}",
                    &report.peer_snapshot_hash[..16.min(report.peer_snapshot_hash.len())]
                );
                println!(
                    "  conflicts: {}  events appended: {}",
                    report.conflicts.len(),
                    report.events_appended
                );
                for c in &report.conflicts {
                    println!("  · {} {} {}", c.kind.as_str(), c.finding_id, c.detail);
                }
            }
        }
        FederationAction::PushResolution {
            frontier,
            conflict_event_id,
            to,
            key,
            vfr_id,
            json,
        } => {
            cmd_federation_push_resolution(frontier, conflict_event_id, to, key, vfr_id, json);
        }
        FederationAction::PeerRemove { frontier, id, json } => {
            let mut project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let before = project.peers.len();
            project.peers.retain(|p| p.id != id);
            if project.peers.len() == before {
                fail(&format!("peer '{id}' not found in registry"));
            }
            repo::save_to_path(&frontier, &project).unwrap_or_else(|e| fail_return(&e));

            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&json!({
                        "ok": true,
                        "command": "federation.peer-remove",
                        "frontier": frontier.display().to_string(),
                        "removed": id,
                        "remaining": project.peers.len(),
                    }))
                    .expect("serialize federation.peer-remove")
                );
            } else {
                println!(
                    "{} peer {} ({} remaining)",
                    style::ok("removed"),
                    id,
                    project.peers.len()
                );
            }
        }
    }
}

/// v0.70: Push a single locally-resolved
/// `frontier.conflict_resolved` event to the peer hub's intake
/// endpoint. The reviewer is the only one who can sign the push —
/// the browser/Workbench never sees the key, same as for proposal
/// signing under Phase R.
///
/// Substrate doctrine: one event per push (no bulk), the hub
/// verifies the signature against an actor record on its own copy
/// of the frontier, the hub refuses unpaired or already-resolved
/// events. The CLI does the matching work locally to fail fast
/// when the consumer's own log is missing the resolution.
fn cmd_federation_push_resolution(
    frontier: PathBuf,
    conflict_event_id: String,
    to: String,
    key: Option<PathBuf>,
    vfr_id: Option<String>,
    json: bool,
) {
    use crate::canonical;
    use crate::sign;

    let project = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));

    let Some(peer) = project.peers.iter().find(|p| p.id == to).cloned() else {
        fail(&format!(
            "peer '{to}' not in registry; run `vela federation peer-add` first"
        ));
    };

    // Locate the resolution event paired with conflict_event_id.
    let Some(resolution) = project
        .events
        .iter()
        .find(|e| {
            e.kind == "frontier.conflict_resolved"
                && e.payload.get("conflict_event_id").and_then(|v| v.as_str())
                    == Some(conflict_event_id.as_str())
        })
        .cloned()
    else {
        fail(&format!(
            "no frontier.conflict_resolved event paired with conflict {conflict_event_id} in {}",
            frontier.display()
        ));
    };

    // Resolve the actor record so we know which public key to send
    // and which key file to load.
    let actor_id = resolution.actor.id.clone();
    let Some(actor) = project.actors.iter().find(|a| a.id == actor_id) else {
        fail(&format!(
            "resolution event's actor.id ({actor_id}) is not in the frontier's actor registry; \
             register the reviewer with `vela actor add` before pushing"
        ));
    };

    // Resolve the private key path. Caller can pass --key explicitly;
    // otherwise look in the conventional locations.
    let key_path = key.unwrap_or_else(|| {
        let home = std::env::var("HOME").unwrap_or_default();
        let base = PathBuf::from(home)
            .join(".config")
            .join("vela")
            .join("keys");
        let safe_id = actor.id.replace([':', '/'], "_");
        let by_actor = base.join(format!("{safe_id}.key"));
        if by_actor.exists() {
            by_actor
        } else {
            base.join("private.key")
        }
    });

    let signing_key = sign::load_signing_key_from_path(&key_path).unwrap_or_else(|e| {
        fail_return(&format!(
            "load private key from {}: {e}",
            key_path.display()
        ))
    });
    let pubkey_hex = sign::pubkey_hex(&signing_key);
    if !pubkey_hex.eq_ignore_ascii_case(&actor.public_key) {
        fail(&format!(
            "private key at {} does not match actor {}'s registered public key. \
             Loaded pubkey {}, expected {}.",
            key_path.display(),
            actor.id,
            &pubkey_hex[..16],
            &actor.public_key[..16]
        ));
    }

    // Sign canonical bytes. Same preimage `verify_event_signature`
    // checks on the hub side.
    let signature_hex = sign::sign_event(&resolution, &signing_key)
        .unwrap_or_else(|e| fail_return(&format!("sign event: {e}")));

    // The wire body is the canonical event JSON without the
    // signature field; the signature travels in the header. This
    // keeps the body byte-exact with what the hub will canonicalize
    // for verification.
    let mut body = resolution.clone();
    body.signature = None;
    let body_value =
        serde_json::to_value(&body).unwrap_or_else(|e| fail_return(&format!("serialize: {e}")));
    let _canonical_check = canonical::to_canonical_bytes(&body_value)
        .unwrap_or_else(|e| fail_return(&format!("canonicalize: {e}")));

    let target_vfr = vfr_id.unwrap_or_else(|| project.frontier_id());
    let url = format!(
        "{}/entries/{}/events",
        peer.url.trim_end_matches('/'),
        target_vfr
    );

    // Same blocking-thread escape pattern as the rest of federation.rs.
    let url_owned = url.clone();
    let pubkey_owned = pubkey_hex.clone();
    let signature_owned = signature_hex.clone();
    let body_owned = body_value.clone();
    let response: Result<(u16, String), String> = std::thread::spawn(move || {
        let client = reqwest::blocking::Client::new();
        let resp = client
            .post(&url_owned)
            .header("X-Vela-Signer-Pubkey", &pubkey_owned)
            .header("X-Vela-Signature", &signature_owned)
            .json(&body_owned)
            .send()
            .map_err(|e| format!("HTTP POST {url_owned}: {e}"))?;
        let status = resp.status().as_u16();
        let text = resp.text().unwrap_or_default();
        Ok((status, text))
    })
    .join()
    .map_err(|_| "push thread panicked".to_string())
    .unwrap_or_else(|e| fail_return(&e));

    let (status, text) = response.unwrap_or_else(|e| fail_return(&e));
    let parsed: serde_json::Value =
        serde_json::from_str(&text).unwrap_or_else(|_| json!({ "raw": text }));

    let accepted = matches!(status, 200..=202);
    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": accepted,
                "command": "federation.push-resolution",
                "frontier": frontier.display().to_string(),
                "peer_id": to,
                "url": url,
                "conflict_event_id": conflict_event_id,
                "event_id": resolution.id,
                "actor_id": actor.id,
                "http_status": status,
                "response": parsed,
            }))
            .expect("serialize federation.push-resolution")
        );
    } else if accepted {
        println!(
            "{} resolution {} pushed to {} (HTTP {})",
            style::ok("ok"),
            &resolution.id[..16.min(resolution.id.len())],
            to,
            status
        );
        println!("  url:    {url}");
        println!("  signer: {} (actor {})", &pubkey_hex[..16], actor.id);
    } else {
        println!("{} push refused (HTTP {})", style::lost("rejected"), status);
        println!("  url:      {url}");
        println!("  response: {text}");
        std::process::exit(1);
    }
}

/// Phase R (v0.5): walk the local Workbench draft queue. The Workbench
/// browser writes unsigned drafts to a queue file; this CLI is the only
/// place where the actor's private key reads its drafts and signs them.
/// The browser never sees the key.
fn cmd_queue(action: QueueAction) {
    use crate::queue;
    match action {
        QueueAction::List { queue_file, json } => {
            let path = queue_file.unwrap_or_else(queue::default_queue_path);
            let q = queue::load(&path).unwrap_or_else(|e| fail_return(&e));
            if json {
                let payload = json!({
                    "ok": true,
                    "command": "queue.list",
                    "queue_file": path.display().to_string(),
                    "schema": q.schema,
                    "actions": q.actions,
                });
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload).expect("failed to serialize queue.list")
                );
            } else {
                println!();
                println!(
                    "  {}",
                    format!("VELA · QUEUE · LIST · {}", path.display())
                        .to_uppercase()
                        .dimmed()
                );
                println!("  {}", style::tick_row(60));
                if q.actions.is_empty() {
                    println!("  (queue is empty)");
                } else {
                    for (idx, action) in q.actions.iter().enumerate() {
                        println!(
                            "  [{idx}] {} → {}  queued {}",
                            action.kind,
                            action.frontier.display(),
                            action.queued_at
                        );
                    }
                }
            }
        }
        QueueAction::Clear { queue_file, json } => {
            let path = queue_file.unwrap_or_else(queue::default_queue_path);
            let dropped = queue::clear(&path).unwrap_or_else(|e| fail_return(&e));
            if json {
                let payload = json!({
                    "ok": true,
                    "command": "queue.clear",
                    "queue_file": path.display().to_string(),
                    "dropped": dropped,
                });
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize queue.clear")
                );
            } else {
                println!("{} dropped {dropped} queued action(s)", style::ok("ok"));
            }
        }
        QueueAction::Sign {
            actor,
            key,
            queue_file,
            yes_to_all,
            json,
        } => {
            let path = queue_file.unwrap_or_else(queue::default_queue_path);
            let q = queue::load(&path).unwrap_or_else(|e| fail_return(&e));
            if q.actions.is_empty() {
                if json {
                    println!("{}", json!({"ok": true, "signed": 0, "remaining": 0}));
                } else {
                    println!("{} queue is empty", style::ok("ok"));
                }
                return;
            }
            let key_hex = std::fs::read_to_string(&key)
                .map(|s| s.trim().to_string())
                .unwrap_or_else(|e| fail_return(&format!("read key {}: {e}", key.display())));
            let signing_key = parse_signing_key(&key_hex);
            let mut signed_count = 0usize;
            let mut remaining = Vec::new();
            for action in q.actions.iter() {
                if !yes_to_all && !confirm_action(action) {
                    remaining.push(action.clone());
                    continue;
                }
                match sign_and_apply(&signing_key, &actor, action) {
                    Ok(report) => {
                        signed_count += 1;
                        if !json {
                            println!(
                                "{} {} on {}  →  {}",
                                style::ok("signed"),
                                action.kind,
                                action.frontier.display(),
                                report
                            );
                        }
                    }
                    Err(error) => {
                        // Keep failed actions in the queue so the user can retry.
                        remaining.push(action.clone());
                        if !json {
                            eprintln!(
                                "{} {} on {}: {error}",
                                style::warn("failed"),
                                action.kind,
                                action.frontier.display()
                            );
                        }
                    }
                }
            }
            queue::replace_actions(&path, remaining.clone()).unwrap_or_else(|e| fail_return(&e));
            if json {
                let payload = json!({
                    "ok": true,
                    "command": "queue.sign",
                    "signed": signed_count,
                    "remaining": remaining.len(),
                });
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload).expect("failed to serialize queue.sign")
                );
            } else {
                println!(
                    "{} signed {signed_count} action(s); {} remaining in queue",
                    style::ok("ok"),
                    remaining.len()
                );
            }
        }
    }
}

fn parse_signing_key(hex_str: &str) -> ed25519_dalek::SigningKey {
    let bytes = hex::decode(hex_str)
        .unwrap_or_else(|e| fail_return(&format!("invalid private-key hex: {e}")));
    let key_bytes: [u8; 32] = bytes
        .try_into()
        .unwrap_or_else(|_| fail_return("private key must be 32 bytes"));
    ed25519_dalek::SigningKey::from_bytes(&key_bytes)
}

fn confirm_action(action: &crate::queue::QueuedAction) -> bool {
    use std::io::{self, BufRead, Write};
    let mut stdout = io::stdout().lock();
    let _ = writeln!(
        stdout,
        "  sign {} on {}? [y/N] ",
        action.kind,
        action.frontier.display()
    );
    let _ = stdout.flush();
    drop(stdout);
    let stdin = io::stdin();
    let mut line = String::new();
    if stdin.lock().read_line(&mut line).is_err() {
        return false;
    }
    matches!(line.trim().to_lowercase().as_str(), "y" | "yes")
}

/// Sign and apply a queued action. Returns a short summary string on
/// success (the resulting `vpr_…` or `vev_…`). The action is signed
/// locally and applied via the same `proposals::*_at_path` functions the
/// CLI uses — no HTTP roundtrip required.
fn sign_and_apply(
    signing_key: &ed25519_dalek::SigningKey,
    actor: &str,
    action: &crate::queue::QueuedAction,
) -> Result<String, String> {
    use crate::events::StateTarget;
    use crate::proposals;
    let args = &action.args;
    match action.kind.as_str() {
        "propose_review" | "propose_note" | "propose_revise_confidence" | "propose_retract" => {
            let kind = match action.kind.as_str() {
                "propose_review" => "finding.review",
                "propose_note" => "finding.note",
                "propose_revise_confidence" => "finding.confidence_revise",
                "propose_retract" => "finding.retract",
                _ => unreachable!(),
            };
            let target_id = args
                .get("target_finding_id")
                .and_then(Value::as_str)
                .ok_or("target_finding_id missing")?;
            let reason = args
                .get("reason")
                .and_then(Value::as_str)
                .ok_or("reason missing")?;
            let payload = match action.kind.as_str() {
                "propose_review" => {
                    let status = args
                        .get("status")
                        .and_then(Value::as_str)
                        .ok_or("status missing")?;
                    json!({"status": status})
                }
                "propose_note" => {
                    let text = args
                        .get("text")
                        .and_then(Value::as_str)
                        .ok_or("text missing")?;
                    json!({"text": text})
                }
                "propose_revise_confidence" => {
                    let new_score = args
                        .get("new_score")
                        .and_then(Value::as_f64)
                        .ok_or("new_score missing")?;
                    json!({"new_score": new_score})
                }
                "propose_retract" => json!({}),
                _ => unreachable!(),
            };
            let created_at = args
                .get("created_at")
                .and_then(Value::as_str)
                .map(String::from)
                .unwrap_or_else(|| chrono::Utc::now().to_rfc3339());
            let mut proposal = proposals::new_proposal(
                kind,
                StateTarget {
                    r#type: "finding".to_string(),
                    id: target_id.to_string(),
                },
                actor,
                "human",
                reason,
                payload,
                Vec::new(),
                Vec::new(),
            );
            proposal.created_at = created_at;
            proposal.id = proposals::proposal_id(&proposal);
            // Sign the proposal locally to validate parity with what the
            // server-side write tool would have signed; the queue-sign
            // path applies via the local file, not via HTTP.
            let _signature = crate::sign::sign_proposal(&proposal, signing_key)?;
            let result = proposals::create_or_apply(&action.frontier, proposal, false)
                .map_err(|e| format!("create_or_apply: {e}"))?;
            Ok(format!("proposal {}", result.proposal_id))
        }
        "accept_proposal" | "reject_proposal" => {
            let proposal_id = args
                .get("proposal_id")
                .and_then(Value::as_str)
                .ok_or("proposal_id missing")?;
            let reason = args
                .get("reason")
                .and_then(Value::as_str)
                .ok_or("reason missing")?;
            let timestamp = args
                .get("timestamp")
                .and_then(Value::as_str)
                .map(String::from)
                .unwrap_or_else(|| chrono::Utc::now().to_rfc3339());
            // Sign for parity; `accept_at_path`/`reject_at_path` apply locally.
            let preimage = json!({
                "action": if action.kind == "accept_proposal" { "accept" } else { "reject" },
                "proposal_id": proposal_id,
                "reviewer_id": actor,
                "reason": reason,
                "timestamp": timestamp,
            });
            let bytes = crate::canonical::to_canonical_bytes(&preimage)?;
            use ed25519_dalek::Signer;
            let _signature = hex::encode(signing_key.sign(&bytes).to_bytes());
            if action.kind == "accept_proposal" {
                let event_id =
                    crate::proposals::accept_at_path(&action.frontier, proposal_id, actor, reason)
                        .map_err(|e| format!("accept_at_path: {e}"))?;
                Ok(format!("event {event_id}"))
            } else {
                crate::proposals::reject_at_path(&action.frontier, proposal_id, actor, reason)
                    .map_err(|e| format!("reject_at_path: {e}"))?;
                Ok(format!("rejected {proposal_id}"))
            }
        }
        other => Err(format!("unsupported queued action kind '{other}'")),
    }
}

/// v0.8: frontier-level metadata commands. Manages cross-frontier
/// dependency declarations on a frontier file. The substrate enforces
/// that any link target of the form `vf_…@vfr_…` references a declared
/// dependency; these commands edit the declaration list.
/// v0.9: typed link addition. Until v0.9 the only way to add a link
/// was to hand-edit JSON; this command is the CLI on-ramp. Links go
/// directly onto `findings[i].links` (links are not a state-changing
/// proposal kind in v0).
/// v0.19: bundled entity resolution. See `crate::entity_resolve` for the
/// table + algorithm. CLI surface is two subcommands: `resolve` (mutates
/// the frontier file) and `list` (read-only inspection of the table).
fn cmd_entity(action: EntityAction) {
    use crate::entity_resolve;
    match action {
        EntityAction::Resolve {
            frontier,
            force,
            json,
        } => {
            let mut p = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let report = entity_resolve::resolve_frontier(&mut p, force);
            repo::save_to_path(&frontier, &p).unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&serde_json::json!({
                        "ok": true,
                        "command": "entity.resolve",
                        "frontier_path": frontier.display().to_string(),
                        "report": report,
                    }))
                    .expect("serialize")
                );
            } else {
                println!(
                    "{} resolved {} of {} entities ({} already, {} unresolved) across {} findings",
                    style::ok("entity"),
                    report.resolved,
                    report.total_entities,
                    report.already_resolved,
                    report.unresolved_count,
                    report.findings_touched,
                );
                let unresolved_summary: std::collections::BTreeSet<&str> = report
                    .per_finding
                    .iter()
                    .flat_map(|f| f.unresolved.iter().map(String::as_str))
                    .collect();
                if !unresolved_summary.is_empty() {
                    let take = unresolved_summary.iter().take(8).collect::<Vec<_>>();
                    println!(
                        "  unresolved (first {}): {}",
                        take.len(),
                        take.iter().copied().cloned().collect::<Vec<_>>().join(", ")
                    );
                }
            }
        }
        EntityAction::List { json } => {
            let entries: Vec<serde_json::Value> = entity_resolve::iter_bundled()
                .map(|(name, etype, source, id)| {
                    serde_json::json!({
                        "canonical_name": name,
                        "entity_type": etype,
                        "source": source,
                        "id": id,
                    })
                })
                .collect();
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&serde_json::json!({
                        "ok": true,
                        "command": "entity.list",
                        "count": entries.len(),
                        "entries": entries,
                    }))
                    .expect("serialize")
                );
            } else {
                println!("{} {} bundled entries", style::ok("entity"), entries.len());
                for e in &entries {
                    println!(
                        "  {:32}  {:18}  {} {}",
                        e["canonical_name"].as_str().unwrap_or("?"),
                        e["entity_type"].as_str().unwrap_or("?"),
                        e["source"].as_str().unwrap_or("?"),
                        e["id"].as_str().unwrap_or("?"),
                    );
                }
            }
        }
    }
}

fn cmd_link(action: LinkAction) {
    use crate::bundle::{Link, LinkRef};
    match action {
        LinkAction::Add {
            frontier,
            from,
            to,
            r#type,
            note,
            inferred_by,
            no_check_target,
            json,
        } => {
            validate_enum_arg("--type", &r#type, bundle::VALID_LINK_TYPES);
            if !["compiler", "reviewer", "author"].contains(&inferred_by.as_str()) {
                fail(&format!(
                    "invalid --inferred-by '{inferred_by}'. Valid: compiler, reviewer, author"
                ));
            }
            let parsed = LinkRef::parse(&to).unwrap_or_else(|e| {
                fail(&format!(
                    "invalid --to '{to}': {e}. Expected vf_<hex> or vf_<hex>@vfr_<hex>"
                ))
            });
            let mut p = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let source_idx = p
                .findings
                .iter()
                .position(|f| f.id == from)
                .unwrap_or_else(|| {
                    fail_return(&format!("--from finding '{from}' not in frontier"))
                });
            if let LinkRef::Local { vf_id } = &parsed
                && !p.findings.iter().any(|f| &f.id == vf_id)
            {
                fail(&format!(
                    "local --to target '{vf_id}' not in frontier; add the target finding first"
                ));
            }
            if let LinkRef::Cross { vfr_id, .. } = &parsed
                && p.dep_for_vfr(vfr_id).is_none()
            {
                fail(&format!(
                    "cross-frontier --to references vfr_id '{vfr_id}' but no matching dep is declared. Run `vela frontier add-dep {vfr_id} --locator <url> --snapshot <hash>` first."
                ));
            }

            // v0.16: best-effort cross-frontier target-status check. The
            // substrate doctrine is "client verifies on read", but at
            // link-add time it's worth a one-shot fetch to warn the user
            // if their target has been superseded. Failure to fetch is
            // a hint, not a hard error — the link still records.
            let mut target_warning: Option<String> = None;
            if let LinkRef::Cross {
                vfr_id: target_vfr,
                vf_id: target_vf,
            } = &parsed
                && !no_check_target
                && let Some(dep) = p.dep_for_vfr(target_vfr)
                && let Some(locator) = dep.locator.as_deref()
                && (locator.starts_with("http://") || locator.starts_with("https://"))
            {
                let client = reqwest::blocking::Client::builder()
                    .timeout(std::time::Duration::from_secs(15))
                    .build()
                    .ok();
                if let Some(client) = client
                    && let Ok(resp) = client.get(locator).send()
                    && resp.status().is_success()
                    && let Ok(dep_project) = resp.json::<crate::project::Project>()
                {
                    if let Some(target_finding) =
                        dep_project.findings.iter().find(|f| &f.id == target_vf)
                    {
                        if target_finding.flags.superseded {
                            target_warning = Some(format!(
                                "warn · cross-frontier target '{target_vf}' in '{target_vfr}' has flags.superseded = true. \
You may be linking to outdated wording. Pull --transitive and inspect the supersedes chain to find the current finding. \
Use --no-check-target to skip this check."
                            ));
                        }
                    } else {
                        target_warning = Some(format!(
                            "warn · cross-frontier target '{target_vf}' not found in dep '{target_vfr}' (fetched from {locator}). \
The target may have been removed or never existed in the pinned snapshot."
                        ));
                    }
                }
            }

            let now = chrono::Utc::now().to_rfc3339_opts(chrono::SecondsFormat::Secs, true);
            let link = Link {
                target: to.clone(),
                link_type: r#type.clone(),
                note: note.clone(),
                inferred_by: inferred_by.clone(),
                created_at: now,
                mechanism: None,
            };
            p.findings[source_idx].links.push(link);
            project::recompute_stats(&mut p);
            repo::save_to_path(&frontier, &p).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "link.add",
                "frontier": frontier.display().to_string(),
                "from": from,
                "to": to,
                "type": r#type,
                "cross_frontier": parsed.is_cross_frontier(),
            });
            if json {
                let mut p2 = payload.clone();
                if let Some(w) = &target_warning
                    && let serde_json::Value::Object(m) = &mut p2
                {
                    m.insert(
                        "target_warning".to_string(),
                        serde_json::Value::String(w.clone()),
                    );
                }
                println!(
                    "{}",
                    serde_json::to_string_pretty(&p2).expect("failed to serialize link.add")
                );
            } else {
                println!(
                    "{} {} --[{}]--> {}{}",
                    style::ok("link"),
                    from,
                    r#type,
                    to,
                    if parsed.is_cross_frontier() {
                        " (cross-frontier)"
                    } else {
                        ""
                    }
                );
                if let Some(w) = target_warning {
                    println!("  {w}");
                }
            }
        }
    }
}

fn cmd_frontier(action: FrontierAction) {
    use crate::project::ProjectDependency;
    use crate::repo;
    match action {
        FrontierAction::New {
            path,
            name,
            description,
            force,
            json,
        } => {
            if path.exists() && !force {
                fail(&format!(
                    "{} already exists; pass --force to overwrite",
                    path.display()
                ));
            }
            let now = chrono::Utc::now().to_rfc3339_opts(chrono::SecondsFormat::Secs, true);
            let project = project::Project {
                vela_version: project::VELA_SCHEMA_VERSION.to_string(),
                schema: project::VELA_SCHEMA_URL.to_string(),
                frontier_id: None,
                project: project::ProjectMeta {
                    name: name.clone(),
                    description: description.clone(),
                    compiled_at: now,
                    compiler: project::VELA_COMPILER_VERSION.to_string(),
                    papers_processed: 0,
                    errors: 0,
                    dependencies: Vec::new(),
                },
                stats: project::ProjectStats::default(),
                findings: Vec::new(),
                sources: Vec::new(),
                evidence_atoms: Vec::new(),
                condition_records: Vec::new(),
                review_events: Vec::new(),
                confidence_updates: Vec::new(),
                events: Vec::new(),
                proposals: Vec::new(),
                proof_state: proposals::ProofState::default(),
                signatures: Vec::new(),
                actors: Vec::new(),
                replications: Vec::new(),
                datasets: Vec::new(),
                code_artifacts: Vec::new(),
                artifacts: Vec::new(),
                predictions: Vec::new(),
                resolutions: Vec::new(),
                peers: Vec::new(),
                negative_results: Vec::new(),
                trajectories: Vec::new(),
            };
            repo::save_to_path(&path, &project).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "frontier.new",
                "path": path.display().to_string(),
                "name": name,
                "schema": project::VELA_SCHEMA_URL,
                "vela_version": env!("CARGO_PKG_VERSION"),
                "next_steps": [
                    "vela finding add <path> --assertion '...' --author 'reviewer:you' --apply",
                    "vela sign generate-keypair --out keys",
                    "vela actor add <path> reviewer:you --pubkey \"$(cat keys/public.key)\"",
                    "vela registry publish <path> --owner reviewer:you --key keys/private.key --locator <url> --to https://vela-hub.fly.dev",
                ],
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize frontier.new")
                );
            } else {
                println!(
                    "{} scaffolded frontier '{name}' at {}",
                    style::ok("frontier"),
                    path.display()
                );
                println!("  next steps:");
                println!(
                    "    1. vela finding add {} --assertion '...' --author 'reviewer:you' --apply",
                    path.display()
                );
                println!("    2. vela sign generate-keypair --out keys");
                println!(
                    "    3. vela actor add {} reviewer:you --pubkey \"$(cat keys/public.key)\"",
                    path.display()
                );
                println!(
                    "    4. vela registry publish {} --owner reviewer:you --key keys/private.key --locator <url> --to https://vela-hub.fly.dev",
                    path.display()
                );
            }
        }
        FrontierAction::Materialize { frontier, json } => {
            let payload = frontier_repo::materialize(&frontier).unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize frontier materialize")
                );
            } else {
                println!(
                    "{} materialized frontier repo at {}",
                    style::ok("frontier"),
                    frontier.display()
                );
            }
        }
        FrontierAction::AddDep {
            frontier,
            vfr_id,
            locator,
            snapshot,
            name,
            json,
        } => {
            let mut p = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            if p.project
                .dependencies
                .iter()
                .any(|d| d.vfr_id.as_deref() == Some(&vfr_id))
            {
                fail(&format!(
                    "cross-frontier dependency '{vfr_id}' already declared; remove it first via `vela frontier remove-dep`"
                ));
            }
            let dep = ProjectDependency {
                name: name.unwrap_or_else(|| vfr_id.clone()),
                source: "vela.hub".into(),
                version: None,
                pinned_hash: None,
                vfr_id: Some(vfr_id.clone()),
                locator: Some(locator.clone()),
                pinned_snapshot_hash: Some(snapshot.clone()),
            };
            p.project.dependencies.push(dep);
            repo::save_to_path(&frontier, &p).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "frontier.add-dep",
                "frontier": frontier.display().to_string(),
                "vfr_id": vfr_id,
                "locator": locator,
                "pinned_snapshot_hash": snapshot,
                "declared_count": p.project.dependencies.len(),
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize frontier.add-dep")
                );
            } else {
                println!(
                    "{} declared cross-frontier dep {vfr_id}",
                    style::ok("frontier")
                );
                println!("  locator:  {locator}");
                println!("  snapshot: {snapshot}");
            }
        }
        FrontierAction::ListDeps { frontier, json } => {
            let p = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let deps: Vec<&ProjectDependency> = p.project.dependencies.iter().collect();
            if json {
                let payload = json!({
                    "ok": true,
                    "command": "frontier.list-deps",
                    "frontier": frontier.display().to_string(),
                    "count": deps.len(),
                    "dependencies": deps,
                });
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize frontier.list-deps")
                );
            } else {
                println!();
                println!(
                    "  {}",
                    format!("VELA · FRONTIER · LIST-DEPS · {}", frontier.display())
                        .to_uppercase()
                        .dimmed()
                );
                println!("  {}", style::tick_row(60));
                if deps.is_empty() {
                    println!("  (no dependencies declared)");
                } else {
                    for d in &deps {
                        let kind = if d.is_cross_frontier() {
                            "cross-frontier"
                        } else {
                            "compile-time"
                        };
                        println!("  · {} [{kind}]", d.name);
                        if let Some(v) = &d.vfr_id {
                            println!("    vfr_id:   {v}");
                        }
                        if let Some(l) = &d.locator {
                            println!("    locator:  {l}");
                        }
                        if let Some(s) = &d.pinned_snapshot_hash {
                            println!("    snapshot: {s}");
                        }
                    }
                }
            }
        }
        FrontierAction::RemoveDep {
            frontier,
            vfr_id,
            json,
        } => {
            let mut p = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            // Refuse if any link still references this vfr_id.
            for f in &p.findings {
                for l in &f.links {
                    if let Ok(crate::bundle::LinkRef::Cross { vfr_id: ref v, .. }) =
                        crate::bundle::LinkRef::parse(&l.target)
                        && v == &vfr_id
                    {
                        fail(&format!(
                            "cannot remove dep '{vfr_id}': finding {} still links to it via {}",
                            f.id, l.target
                        ));
                    }
                }
            }
            let before = p.project.dependencies.len();
            p.project
                .dependencies
                .retain(|d| d.vfr_id.as_deref() != Some(&vfr_id));
            let removed = before - p.project.dependencies.len();
            if removed == 0 {
                fail(&format!("no cross-frontier dependency '{vfr_id}' found"));
            }
            repo::save_to_path(&frontier, &p).unwrap_or_else(|e| fail_return(&e));
            let payload = json!({
                "ok": true,
                "command": "frontier.remove-dep",
                "frontier": frontier.display().to_string(),
                "vfr_id": vfr_id,
                "removed": removed,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize frontier.remove-dep")
                );
            } else {
                println!(
                    "{} removed cross-frontier dep {vfr_id}",
                    style::ok("frontier")
                );
            }
        }
        FrontierAction::RefreshDeps {
            frontier,
            from,
            dry_run,
            json,
        } => {
            let mut p = repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));
            let cross_deps: Vec<String> = p
                .project
                .dependencies
                .iter()
                .filter_map(|d| d.vfr_id.clone())
                .collect();
            if cross_deps.is_empty() {
                if json {
                    println!(
                        "{}",
                        serde_json::to_string_pretty(&json!({
                            "ok": true,
                            "command": "frontier.refresh-deps",
                            "frontier": frontier.display().to_string(),
                            "from": from,
                            "dry_run": dry_run,
                            "deps": [],
                            "summary": { "total": 0, "refreshed": 0, "unchanged": 0, "missing": 0, "unreachable": 0 },
                        })).expect("serialize")
                    );
                } else {
                    println!(
                        "{} no cross-frontier deps declared in {}",
                        style::ok("frontier"),
                        frontier.display()
                    );
                }
                return;
            }
            let client = reqwest::blocking::Client::builder()
                .timeout(std::time::Duration::from_secs(20))
                .build()
                .unwrap_or_else(|e| fail_return(&format!("http client init failed: {e}")));
            let base = from.trim_end_matches('/');
            #[derive(serde::Deserialize)]
            struct HubEntry {
                latest_snapshot_hash: String,
            }
            let mut per_dep: Vec<serde_json::Value> = Vec::new();
            let (mut refreshed, mut unchanged, mut missing, mut unreachable) =
                (0u32, 0u32, 0u32, 0u32);
            for vfr in &cross_deps {
                let url = format!("{base}/entries/{vfr}");
                let resp = client.get(&url).send();
                let outcome = match resp {
                    Ok(r) if r.status().as_u16() == 404 => {
                        missing += 1;
                        json!({ "vfr_id": vfr, "status": "missing", "url": url })
                    }
                    Ok(r) if !r.status().is_success() => {
                        unreachable += 1;
                        json!({ "vfr_id": vfr, "status": "unreachable", "http_status": r.status().as_u16() })
                    }
                    Err(e) => {
                        unreachable += 1;
                        json!({ "vfr_id": vfr, "status": "unreachable", "error": e.to_string() })
                    }
                    Ok(r) => match r.json::<HubEntry>() {
                        Err(e) => {
                            unreachable += 1;
                            json!({ "vfr_id": vfr, "status": "unreachable", "error": format!("invalid hub response: {e}") })
                        }
                        Ok(entry) => {
                            // Locate the dep in our project to compare + (maybe) mutate.
                            match p
                                .project
                                .dependencies
                                .iter()
                                .position(|d| d.vfr_id.as_deref() == Some(vfr.as_str()))
                            {
                                None => {
                                    unreachable += 1;
                                    json!({ "vfr_id": vfr, "status": "unreachable", "error": "dep disappeared mid-scan" })
                                }
                                Some(idx) => {
                                    let local_pin =
                                        p.project.dependencies[idx].pinned_snapshot_hash.clone();
                                    let new_pin = entry.latest_snapshot_hash;
                                    if local_pin.as_deref() == Some(new_pin.as_str()) {
                                        unchanged += 1;
                                        json!({ "vfr_id": vfr, "status": "unchanged", "snapshot": new_pin })
                                    } else {
                                        if !dry_run {
                                            p.project.dependencies[idx].pinned_snapshot_hash =
                                                Some(new_pin.clone());
                                        }
                                        refreshed += 1;
                                        json!({
                                            "vfr_id": vfr,
                                            "status": "refreshed",
                                            "old_snapshot": local_pin,
                                            "new_snapshot": new_pin,
                                        })
                                    }
                                }
                            }
                        }
                    },
                };
                per_dep.push(outcome);
            }
            if !dry_run && refreshed > 0 {
                repo::save_to_path(&frontier, &p).unwrap_or_else(|e| fail_return(&e));
            }
            let payload = json!({
                "ok": true,
                "command": "frontier.refresh-deps",
                "frontier": frontier.display().to_string(),
                "from": from,
                "dry_run": dry_run,
                "deps": per_dep,
                "summary": {
                    "total": cross_deps.len(),
                    "refreshed": refreshed,
                    "unchanged": unchanged,
                    "missing": missing,
                    "unreachable": unreachable,
                },
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize frontier.refresh-deps")
                );
            } else {
                let mode = if dry_run { " (dry-run)" } else { "" };
                println!(
                    "{} refresh-deps{mode} · {} total · {refreshed} refreshed · {unchanged} unchanged · {missing} missing · {unreachable} unreachable",
                    style::ok("frontier"),
                    cross_deps.len()
                );
                for d in &per_dep {
                    let vfr = d["vfr_id"].as_str().unwrap_or("?");
                    let status = d["status"].as_str().unwrap_or("?");
                    match status {
                        "refreshed" => println!(
                            "  {vfr}  refreshed  {} → {}",
                            d["old_snapshot"]
                                .as_str()
                                .unwrap_or("(none)")
                                .chars()
                                .take(16)
                                .collect::<String>(),
                            d["new_snapshot"]
                                .as_str()
                                .unwrap_or("?")
                                .chars()
                                .take(16)
                                .collect::<String>(),
                        ),
                        "unchanged" => println!("  {vfr}  unchanged"),
                        "missing" => println!("  {vfr}  missing on hub"),
                        _ => println!("  {vfr}  unreachable"),
                    }
                }
            }
        }
        FrontierAction::Diff {
            frontier,
            since,
            week,
            json,
        } => cmd_frontier_diff(&frontier, since.as_deref(), week.as_deref(), json),
    }
}

fn cmd_repo(action: RepoAction) {
    match action {
        RepoAction::Status { frontier, json } => {
            let payload = frontier_repo::repo_status(&frontier).unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize repo status")
                );
            } else {
                let summary = payload.get("summary").unwrap_or(&Value::Null);
                let freshness = payload.get("freshness").unwrap_or(&Value::Null);
                println!("vela repo status");
                println!("  frontier: {}", frontier.display());
                println!(
                    "  events:   {}",
                    summary
                        .get("accepted_events")
                        .and_then(Value::as_u64)
                        .unwrap_or_default()
                );
                println!(
                    "  open proposals: {}",
                    summary
                        .get("open_proposals")
                        .and_then(Value::as_u64)
                        .unwrap_or_default()
                );
                println!(
                    "  state:    {}",
                    freshness
                        .get("materialized_state")
                        .and_then(Value::as_str)
                        .unwrap_or("unknown")
                );
                println!(
                    "  proof:    {}",
                    freshness
                        .get("proof")
                        .and_then(Value::as_str)
                        .unwrap_or("unknown")
                );
            }
        }
        RepoAction::Doctor { frontier, json } => {
            let payload = frontier_repo::repo_doctor(&frontier).unwrap_or_else(|e| fail_return(&e));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize repo doctor")
                );
            } else {
                let ok = payload.get("ok").and_then(Value::as_bool) == Some(true);
                let issues = payload
                    .get("issues")
                    .and_then(Value::as_array)
                    .map_or(0, Vec::len);
                println!("vela repo doctor");
                println!("  frontier: {}", frontier.display());
                println!("  status:   {}", if ok { "ok" } else { "needs attention" });
                println!("  issues:   {issues}");
            }
        }
    }
}

fn cmd_proof_verify(frontier: &Path, json_output: bool) {
    let payload = frontier_repo::proof_verify(frontier).unwrap_or_else(|e| fail_return(&e));
    if json_output {
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize proof verify")
        );
        if payload.get("ok").and_then(Value::as_bool) != Some(true) {
            std::process::exit(1);
        }
    } else {
        let ok = payload.get("ok").and_then(Value::as_bool) == Some(true);
        println!("vela proof verify");
        println!("  frontier: {}", frontier.display());
        println!("  status:   {}", if ok { "ok" } else { "failed" });
        if let Some(issues) = payload.get("issues").and_then(Value::as_array) {
            for issue in issues {
                if let Some(message) = issue.get("message").and_then(Value::as_str) {
                    println!("  issue:    {message}");
                }
            }
        }
        if !ok {
            std::process::exit(1);
        }
    }
}

fn cmd_proof_explain(frontier: &Path) {
    let text = frontier_repo::proof_explain(frontier).unwrap_or_else(|e| fail_return(&e));
    print!("{text}");
}

/// v0.32: structured diff of findings added/updated/contradicted in a
/// time window. Read-only over canonical state; does not modify the
/// frontier and does not need a signing key.
///
/// Window resolution priority: `--since` > `--week` > current ISO week.
/// If `--since` is given, the upper bound is "now" (UTC); the diff
/// covers `[since, now)`. If `--week` is given (or defaulted), the
/// window is `[Mon 00:00 UTC, next Mon 00:00 UTC)`.
fn cmd_frontier_diff(frontier: &Path, since: Option<&str>, week: Option<&str>, json: bool) {
    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));

    // ── Resolve the window ──
    let now = chrono::Utc::now();
    let (window_start, window_end, week_label): (
        chrono::DateTime<chrono::Utc>,
        chrono::DateTime<chrono::Utc>,
        Option<String>,
    ) = if let Some(s) = since {
        let parsed = chrono::DateTime::parse_from_rfc3339(s)
            .map(|d| d.with_timezone(&chrono::Utc))
            .unwrap_or_else(|e| fail_return(&format!("invalid --since timestamp '{s}': {e}")));
        (parsed, now, None)
    } else {
        let key = week
            .map(str::to_owned)
            .unwrap_or_else(|| iso_week_key_for(now.date_naive()));
        let (start, end) = iso_week_bounds(&key)
            .unwrap_or_else(|e| fail_return(&format!("invalid --week '{key}': {e}")));
        (start, end, Some(key))
    };

    // ── Bucket findings ──
    let mut added: Vec<&crate::bundle::FindingBundle> = Vec::new();
    let mut updated: Vec<&crate::bundle::FindingBundle> = Vec::new();
    let mut new_contradictions: Vec<&crate::bundle::FindingBundle> = Vec::new();
    let mut cumulative: usize = 0;

    for f in &project.findings {
        let created = chrono::DateTime::parse_from_rfc3339(&f.created)
            .map(|d| d.with_timezone(&chrono::Utc))
            .ok();
        let updated_ts = f
            .updated
            .as_deref()
            .and_then(|u| chrono::DateTime::parse_from_rfc3339(u).ok())
            .map(|d| d.with_timezone(&chrono::Utc));

        if let Some(c) = created
            && c < window_end
        {
            cumulative += 1;
        }

        if let Some(c) = created
            && c >= window_start
            && c < window_end
        {
            added.push(f);
            let is_tension = f.flags.contested || f.assertion.assertion_type == "tension";
            if is_tension {
                new_contradictions.push(f);
            }
            continue;
        }
        if let Some(u) = updated_ts
            && u >= window_start
            && u < window_end
        {
            updated.push(f);
        }
    }

    // ── Render ──
    let summary_for = |list: &[&crate::bundle::FindingBundle]| -> Vec<serde_json::Value> {
        list.iter()
            .map(|f| {
                json!({
                    "id": f.id,
                    "assertion": f.assertion.text,
                    "evidence_type": f.evidence.evidence_type,
                    "confidence": f.confidence.score,
                    "doi": f.provenance.doi,
                    "pmid": f.provenance.pmid,
                })
            })
            .collect()
    };

    let payload = json!({
        "ok": true,
        "command": "frontier.diff",
        "frontier": frontier.display().to_string(),
        "frontier_id": project.frontier_id,
        "window": {
            "start": window_start.to_rfc3339_opts(chrono::SecondsFormat::Secs, true),
            "end": window_end.to_rfc3339_opts(chrono::SecondsFormat::Secs, true),
            "iso_week": week_label,
        },
        "totals": {
            "added": added.len(),
            "updated": updated.len(),
            "new_contradictions": new_contradictions.len(),
            "cumulative_claims": cumulative,
        },
        "added": summary_for(&added),
        "updated": summary_for(&updated),
        "new_contradictions": summary_for(&new_contradictions),
    });

    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize frontier.diff")
        );
        return;
    }

    let label = week_label
        .clone()
        .unwrap_or_else(|| format!("since {}", window_start.format("%Y-%m-%d %H:%M UTC")));
    println!();
    println!(
        "  {}",
        format!("VELA · FRONTIER · DIFF · {label}")
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    println!(
        "  range:           {} → {}",
        window_start.format("%Y-%m-%d %H:%M"),
        window_end.format("%Y-%m-%d %H:%M")
    );
    println!("  added:           {}", added.len());
    println!("  updated:         {}", updated.len());
    println!("  contradictions:  {}", new_contradictions.len());
    println!("  cumulative:      {cumulative}");
    if added.is_empty() && updated.is_empty() {
        println!();
        println!("  (quiet window — no findings added or updated)");
    } else {
        println!();
        println!("  added:");
        for f in &added {
            println!(
                "    · {}  {}",
                f.id.dimmed(),
                truncate(&f.assertion.text, 88)
            );
        }
        if !updated.is_empty() {
            println!();
            println!("  updated:");
            for f in &updated {
                println!(
                    "    · {}  {}",
                    f.id.dimmed(),
                    truncate(&f.assertion.text, 88)
                );
            }
        }
    }
}

fn truncate(s: &str, n: usize) -> String {
    if s.chars().count() <= n {
        s.to_string()
    } else {
        let mut out: String = s.chars().take(n.saturating_sub(1)).collect();
        out.push('…');
        out
    }
}

/// ISO 8601 week key in `YYYY-Www` form for a given calendar date.
fn iso_week_key_for(d: chrono::NaiveDate) -> String {
    use chrono::Datelike;
    let iso = d.iso_week();
    format!("{:04}-W{:02}", iso.year(), iso.week())
}

/// Resolve `YYYY-Www` to its UTC bounds:
/// `[Monday 00:00 UTC, next Monday 00:00 UTC)`.
fn iso_week_bounds(
    key: &str,
) -> Result<(chrono::DateTime<chrono::Utc>, chrono::DateTime<chrono::Utc>), String> {
    let (year_str, week_str) = key
        .split_once("-W")
        .ok_or_else(|| format!("expected YYYY-Www, got '{key}'"))?;
    let year: i32 = year_str
        .parse()
        .map_err(|e| format!("bad year in '{key}': {e}"))?;
    let week: u32 = week_str
        .parse()
        .map_err(|e| format!("bad week in '{key}': {e}"))?;
    let monday = chrono::NaiveDate::from_isoywd_opt(year, week, chrono::Weekday::Mon)
        .ok_or_else(|| format!("invalid ISO week: {key}"))?;
    let next_monday = monday + chrono::Duration::days(7);
    let start = monday.and_hms_opt(0, 0, 0).expect("00:00 valid").and_utc();
    let end = next_monday
        .and_hms_opt(0, 0, 0)
        .expect("00:00 valid")
        .and_utc();
    Ok((start, end))
}

/// Phase S (v0.5): registry CLI — publish/pull a frontier through a
/// signed manifest. Verifiable distribution: any third party can pull
/// and confirm the snapshot and event-log hashes match what the owner
/// signed.
fn cmd_registry(action: RegistryAction) {
    use crate::registry;
    let default_registry = || -> PathBuf {
        let home = std::env::var("HOME").unwrap_or_else(|_| ".".to_string());
        PathBuf::from(home)
            .join(".vela")
            .join("registry")
            .join("entries.json")
    };
    match action {
        RegistryAction::DependsOn { vfr_id, from, json } => {
            let base = from.trim_end_matches('/');
            let url = format!("{base}/entries/{vfr_id}/depends-on");
            let client = reqwest::blocking::Client::builder()
                .timeout(std::time::Duration::from_secs(30))
                .build()
                .unwrap_or_else(|e| fail_return(&format!("http client init: {e}")));
            let resp = client
                .get(&url)
                .send()
                .unwrap_or_else(|e| fail_return(&format!("GET {url}: {e}")));
            if !resp.status().is_success() {
                fail(&format!("GET {url}: HTTP {}", resp.status()));
            }
            let body: serde_json::Value = resp
                .json()
                .unwrap_or_else(|e| fail_return(&format!("parse response: {e}")));
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&body).expect("serialize")
                );
            } else {
                let dependents = body
                    .get("dependents")
                    .and_then(|v| v.as_array())
                    .cloned()
                    .unwrap_or_default();
                let count = dependents.len();
                println!(
                    "{} {count} {} on {vfr_id}",
                    style::ok("registry"),
                    if count == 1 {
                        "frontier depends"
                    } else {
                        "frontiers depend"
                    },
                );
                for e in &dependents {
                    let v = e.get("vfr_id").and_then(|v| v.as_str()).unwrap_or("?");
                    let n = e.get("name").and_then(|v| v.as_str()).unwrap_or("?");
                    let o = e
                        .get("owner_actor_id")
                        .and_then(|v| v.as_str())
                        .unwrap_or("?");
                    println!("  {v}  {n}  ({o})");
                }
            }
        }
        RegistryAction::Mirror {
            vfr_id,
            from,
            to,
            json,
        } => {
            let src_base = from.trim_end_matches('/');
            let dst_base = to.trim_end_matches('/');
            let src_url = format!("{src_base}/entries/{vfr_id}");
            let dst_url = format!("{dst_base}/entries");
            let client = reqwest::blocking::Client::builder()
                .timeout(std::time::Duration::from_secs(30))
                .build()
                .unwrap_or_else(|e| fail_return(&format!("http client init: {e}")));

            let entry: serde_json::Value = client
                .get(&src_url)
                .send()
                .unwrap_or_else(|e| fail_return(&format!("GET {src_url}: {e}")))
                .error_for_status()
                .unwrap_or_else(|e| fail_return(&format!("GET {src_url}: {e}")))
                .json()
                .unwrap_or_else(|e| fail_return(&format!("parse {src_url}: {e}")));

            let resp = client
                .post(&dst_url)
                .header("content-type", "application/json")
                .body(
                    serde_json::to_vec(&entry)
                        .unwrap_or_else(|e| fail_return(&format!("serialize: {e}"))),
                )
                .send()
                .unwrap_or_else(|e| fail_return(&format!("POST {dst_url}: {e}")));
            let status = resp.status();
            if !status.is_success() {
                let body = resp.text().unwrap_or_default();
                fail(&format!(
                    "POST {dst_url}: HTTP {status}: {}",
                    body.chars().take(300).collect::<String>()
                ));
            }
            let body: serde_json::Value = resp
                .json()
                .unwrap_or_else(|e| fail_return(&format!("parse POST response: {e}")));
            let duplicate = body
                .get("duplicate")
                .and_then(serde_json::Value::as_bool)
                .unwrap_or(false);
            let payload = json!({
                "ok": true,
                "command": "registry.mirror",
                "vfr_id": vfr_id,
                "from": src_base,
                "to": dst_base,
                "duplicate_on_destination": duplicate,
                "destination_response": body,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload).expect("serialize")
                );
            } else {
                println!(
                    "{} mirrored {vfr_id} from {src_base} → {dst_base}{}",
                    style::ok("registry"),
                    if duplicate {
                        " (duplicate; signature already known)"
                    } else {
                        " (fresh insert)"
                    }
                );
            }
        }
        RegistryAction::List { from, json } => {
            // Phase γ-hub (v0.7): `--from <https://...>` fetches the
            // registry over HTTPS; bare paths and file:// resolve locally.
            let (label, registry_data) = match &from {
                Some(loc) if loc.starts_with("http") => (
                    loc.clone(),
                    registry::load_any(loc).unwrap_or_else(|e| fail_return(&e)),
                ),
                Some(loc) => {
                    let p = registry::resolve_local(loc).unwrap_or_else(|e| fail_return(&e));
                    (
                        p.display().to_string(),
                        registry::load_local(&p).unwrap_or_else(|e| fail_return(&e)),
                    )
                }
                None => {
                    let p = default_registry();
                    (
                        p.display().to_string(),
                        registry::load_local(&p).unwrap_or_else(|e| fail_return(&e)),
                    )
                }
            };
            let r = registry_data;
            let path_label = label;
            if json {
                let payload = json!({
                    "ok": true,
                    "command": "registry.list",
                    "registry": path_label,
                    "entry_count": r.entries.len(),
                    "entries": r.entries,
                });
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize registry.list")
                );
            } else {
                println!();
                println!(
                    "  {}",
                    format!("VELA · REGISTRY · LIST · {}", path_label)
                        .to_uppercase()
                        .dimmed()
                );
                println!("  {}", style::tick_row(60));
                if r.entries.is_empty() {
                    println!("  (registry is empty)");
                } else {
                    for entry in &r.entries {
                        println!(
                            "  {} {} ({})  by {}  published {}",
                            entry.vfr_id,
                            entry.name,
                            entry.network_locator,
                            entry.owner_actor_id,
                            entry.signed_publish_at
                        );
                    }
                }
            }
        }
        RegistryAction::Publish {
            frontier,
            owner,
            key,
            locator,
            to,
            json,
        } => {
            // Read and parse the private key first so we can derive
            // the pubkey before we look at the actor registry.
            let key_hex = std::fs::read_to_string(&key)
                .map(|s| s.trim().to_string())
                .unwrap_or_else(|e| fail_return(&format!("read key {}: {e}", key.display())));
            let signing_key = parse_signing_key(&key_hex);
            let derived = hex::encode(signing_key.verifying_key().to_bytes());

            // Load frontier and look up (or auto-register) the owner.
            let mut frontier_data =
                repo::load_from_path(&frontier).unwrap_or_else(|e| fail_return(&e));

            let pubkey = match frontier_data.actors.iter().find(|actor| actor.id == owner) {
                Some(actor) => actor.public_key.clone(),
                None => {
                    // v0.101 auto-bootstrap: an unregistered owner who
                    // supplies a valid private key gets registered on
                    // the fly using the derived pubkey. Eliminates the
                    // "publish fails, run `vela actor add`, retry" loop
                    // for fresh frontiers. The auto-registration is
                    // recorded as a normal actor entry; subsequent
                    // publishes go through the registered-path.
                    eprintln!(
                        "  vela registry publish · auto-registering actor {owner} (derived pubkey {})",
                        &derived[..16]
                    );
                    frontier_data.actors.push(sign::ActorRecord {
                        id: owner.clone(),
                        public_key: derived.clone(),
                        algorithm: "ed25519".to_string(),
                        created_at: chrono::Utc::now().to_rfc3339(),
                        tier: None,
                        orcid: None,
                        access_clearance: None,
                    });
                    repo::save_to_path(&frontier, &frontier_data)
                        .unwrap_or_else(|e| fail_return(&format!("save actor: {e}")));
                    derived.clone()
                }
            };

            // Compute snapshot+event_log hashes after any auto-
            // registration write so the published manifest reflects
            // the actor record we just persisted.
            let snapshot_hash = events::snapshot_hash(&frontier_data);
            let event_log_hash = events::event_log_hash(&frontier_data.events);
            let vfr_id = frontier_data.frontier_id();
            let name = frontier_data.project.name.clone();

            // Sanity check: pubkey on disk matches pubkey in the registry.
            if derived != pubkey {
                fail(&format!(
                    "private key does not match registered pubkey for owner '{owner}'"
                ));
            }

            // Phase A2 (v0.7): when `--to` is an HTTPS URL we POST the
            // signed entry to a hub; otherwise we resolve a local file
            // and append. v0.55: the locator can be auto-filled when
            // publishing to a remote hub: the hub's own
            // `/entries/<vfr>/snapshot` endpoint is the canonical fetch
            // location once substrate is promoted into event/projection
            // tables.
            let to_is_remote = matches!(
                to.as_deref(),
                Some(loc) if loc.starts_with("http://") || loc.starts_with("https://")
            );
            let resolved_locator = match locator {
                Some(l) => l,
                None => {
                    if to_is_remote {
                        let hub = to.as_deref().unwrap().trim_end_matches('/');
                        let hub_root = hub.trim_end_matches("/entries");
                        format!("{hub_root}/entries/{vfr_id}/snapshot")
                    } else {
                        fail_return(
                            "--locator is required for local publishes; pass e.g. \
                             --locator file:///path/to/frontier.json or an HTTPS URL.",
                        )
                    }
                }
            };

            let mut entry = registry::RegistryEntry {
                schema: registry::ENTRY_SCHEMA.to_string(),
                vfr_id: vfr_id.clone(),
                name: name.clone(),
                owner_actor_id: owner.clone(),
                owner_pubkey: pubkey,
                latest_snapshot_hash: snapshot_hash,
                latest_event_log_hash: event_log_hash,
                network_locator: resolved_locator,
                signed_publish_at: chrono::Utc::now().to_rfc3339(),
                signature: String::new(),
            };
            entry.signature =
                registry::sign_entry(&entry, &signing_key).unwrap_or_else(|e| fail_return(&e));

            let (registry_label, duplicate) = if to_is_remote {
                let hub_url = to.clone().unwrap();
                // v0.55: include the substrate inline so the hub can
                // verify hashes, store the snapshot export, and promote
                // event/projection rows for live reads.
                let resp = registry::publish_remote(&entry, &hub_url, Some(&frontier_data))
                    .unwrap_or_else(|e| fail_return(&e));
                (hub_url, resp.duplicate)
            } else {
                let registry_path = match &to {
                    Some(loc) => registry::resolve_local(loc).unwrap_or_else(|e| fail_return(&e)),
                    None => default_registry(),
                };
                registry::publish_entry(&registry_path, entry.clone())
                    .unwrap_or_else(|e| fail_return(&e));
                (registry_path.display().to_string(), false)
            };

            let payload = json!({
                "ok": true,
                "command": "registry.publish",
                "registry": registry_label,
                "vfr_id": vfr_id,
                "name": name,
                "owner": owner,
                "snapshot_hash": entry.latest_snapshot_hash,
                "event_log_hash": entry.latest_event_log_hash,
                "signed_publish_at": entry.signed_publish_at,
                "signature": entry.signature,
                "duplicate": duplicate,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize registry.publish")
                );
            } else {
                let dup_suffix = if duplicate { " (duplicate, no-op)" } else { "" };
                println!(
                    "{} published {vfr_id} → {}{}",
                    style::ok("registry"),
                    registry_label,
                    dup_suffix
                );
                println!("  snapshot:  {}", entry.latest_snapshot_hash);
                println!("  event_log: {}", entry.latest_event_log_hash);
                println!("  signature: {}…", &entry.signature[..16]);
            }
        }
        RegistryAction::Pull {
            vfr_id,
            from,
            out,
            transitive,
            depth,
            json,
        } => {
            // Phase γ-hub (v0.7): both the registry and the frontier
            // can live behind https:// now. Local file:// and bare-path
            // remain supported.
            let (registry_label, registry_data) = match &from {
                Some(loc) if loc.starts_with("http") => (
                    loc.clone(),
                    registry::load_any(loc).unwrap_or_else(|e| fail_return(&e)),
                ),
                Some(loc) => {
                    let p = registry::resolve_local(loc).unwrap_or_else(|e| fail_return(&e));
                    (
                        p.display().to_string(),
                        registry::load_local(&p).unwrap_or_else(|e| fail_return(&e)),
                    )
                }
                None => {
                    let p = default_registry();
                    (
                        p.display().to_string(),
                        registry::load_local(&p).unwrap_or_else(|e| fail_return(&e)),
                    )
                }
            };
            let entry = registry::find_latest(&registry_data, &vfr_id)
                .unwrap_or_else(|| fail_return(&format!("{vfr_id} not found in registry")));

            if transitive {
                // v0.8: --transitive walks the dep graph. `out` is
                // interpreted as a directory; the primary lands at
                // out/<vfr>.json, deps at out/<dep_vfr>.json.
                let result = registry::pull_transitive(&registry_data, &vfr_id, &out, depth)
                    .unwrap_or_else(|e| fail_return(&format!("transitive pull failed: {e}")));

                let dep_paths_json: serde_json::Value = serde_json::Value::Object(
                    result
                        .deps
                        .iter()
                        .map(|(k, v)| (k.clone(), serde_json::json!(v.display().to_string())))
                        .collect(),
                );
                let payload = json!({
                    "ok": true,
                    "command": "registry.pull",
                    "registry": registry_label,
                    "vfr_id": vfr_id,
                    "transitive": true,
                    "depth": depth,
                    "out_dir": out.display().to_string(),
                    "primary": result.primary_path.display().to_string(),
                    "verified": result.verified,
                    "deps": dep_paths_json,
                });
                if json {
                    println!(
                        "{}",
                        serde_json::to_string_pretty(&payload)
                            .expect("failed to serialize registry.pull")
                    );
                } else {
                    println!(
                        "{} pulled {vfr_id} (transitive) → {}",
                        style::ok("registry"),
                        out.display()
                    );
                    println!("  verified {} frontier(s):", result.verified.len());
                    for v in &result.verified {
                        println!("    · {v}");
                    }
                    println!("  every cross-frontier dependency's pinned snapshot hash matched");
                }
                return;
            }

            // Fetch the frontier from its locator (file:// or https://)
            // and verify hashes + signature.
            registry::fetch_frontier_to_prefer_event_hub(&entry, from.as_deref(), &out)
                .unwrap_or_else(|e| fail_return(&format!("fetch frontier: {e}")));
            registry::verify_pull(&entry, &out).unwrap_or_else(|e| {
                let _ = std::fs::remove_file(&out);
                fail_return(&format!("pull verification failed: {e}"))
            });

            let payload = json!({
                "ok": true,
                "command": "registry.pull",
                "registry": registry_label,
                "vfr_id": vfr_id,
                "out": out.display().to_string(),
                "snapshot_hash": entry.latest_snapshot_hash,
                "event_log_hash": entry.latest_event_log_hash,
                "verified": true,
            });
            if json {
                println!(
                    "{}",
                    serde_json::to_string_pretty(&payload)
                        .expect("failed to serialize registry.pull")
                );
            } else {
                println!(
                    "{} pulled {vfr_id} → {}",
                    style::ok("registry"),
                    out.display()
                );
                println!("  verified snapshot+event_log hashes match registry; signature ok");
            }
        }
    }
}

fn print_stats_json(path: &Path) {
    let frontier = load_frontier_or_fail(path);
    let source_hash = hash_path_or_fail(path);
    let payload = json!({
        "ok": true,
        "command": "stats",
        "schema_version": project::VELA_SCHEMA_VERSION,
        "frontier": {
            "name": &frontier.project.name,
            "description": &frontier.project.description,
            "source": path.display().to_string(),
            "hash": format!("sha256:{source_hash}"),
            "compiled_at": &frontier.project.compiled_at,
            "compiler": &frontier.project.compiler,
            "papers_processed": frontier.project.papers_processed,
            "errors": frontier.project.errors,
        },
        "stats": frontier.stats,
        "proposals": proposals::summary(&frontier),
        "proof_state": frontier.proof_state,
    });
    println!(
        "{}",
        serde_json::to_string_pretty(&payload).expect("failed to serialize stats")
    );
}

fn cmd_search(
    source: Option<&Path>,
    query: &str,
    entity: Option<&str>,
    assertion_type: Option<&str>,
    all: Option<&Path>,
    limit: usize,
    json_output: bool,
) {
    if let Some(dir) = all {
        search::run_all(dir, query, entity, assertion_type, limit);
        return;
    }
    let Some(src) = source else {
        fail("Provide --source <frontier> or --all <directory>.");
    };
    if json_output {
        let results = search::search(src, query, entity, assertion_type, limit);
        let loaded = load_frontier_or_fail(src);
        let source_hash = hash_path_or_fail(src);
        let payload = json!({
            "ok": true,
            "command": "search",
            "schema_version": project::VELA_SCHEMA_VERSION,
            "query": query,
            "frontier": {
                "name": &loaded.project.name,
                "source": src.display().to_string(),
                "hash": format!("sha256:{source_hash}"),
            },
            "filters": {
                "entity": entity,
                "assertion_type": assertion_type,
                "limit": limit,
            },
            "count": results.len(),
            "results": results.iter().map(|result| json!({
                "id": &result.id,
                "score": result.score,
                "assertion": &result.assertion,
                "assertion_type": &result.assertion_type,
                "confidence": result.confidence,
                "entities": &result.entities,
                "doi": &result.doi,
            })).collect::<Vec<_>>()
        });
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize search results")
        );
    } else {
        search::run(src, query, entity, assertion_type, limit);
    }
}

fn cmd_tensions(source: &Path, both_high: bool, cross_domain: bool, top: usize, json_output: bool) {
    let frontier = load_frontier_or_fail(source);
    let result = tensions::analyze(&frontier, both_high, cross_domain, top);
    if json_output {
        let source_hash = hash_path_or_fail(source);
        let payload = json!({
            "ok": true,
            "command": "tensions",
            "schema_version": project::VELA_SCHEMA_VERSION,
            "frontier": {
                "name": &frontier.project.name,
                "source": source.display().to_string(),
                "hash": format!("sha256:{source_hash}"),
            },
            "filters": {
                "both_high": both_high,
                "cross_domain": cross_domain,
                "top": top,
            },
            "count": result.len(),
            "tensions": result.iter().map(|t| json!({
                "score": t.score,
                "resolved": t.resolved,
                "superseding_id": &t.superseding_id,
                "finding_a": {
                    "id": &t.finding_a.id,
                    "assertion": &t.finding_a.assertion,
                    "confidence": t.finding_a.confidence,
                    "assertion_type": &t.finding_a.assertion_type,
                    "citation_count": t.finding_a.citation_count,
                    "contradicts_count": t.finding_a.contradicts_count,
                },
                "finding_b": {
                    "id": &t.finding_b.id,
                    "assertion": &t.finding_b.assertion,
                    "confidence": t.finding_b.confidence,
                    "assertion_type": &t.finding_b.assertion_type,
                    "citation_count": t.finding_b.citation_count,
                    "contradicts_count": t.finding_b.contradicts_count,
                }
            })).collect::<Vec<_>>()
        });
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize tensions")
        );
    } else {
        tensions::print_tensions(&result);
    }
}

fn cmd_gaps(action: GapsAction) {
    match action {
        GapsAction::Rank {
            frontier,
            top,
            domain,
            json,
        } => cmd_gap_rank(&frontier, top, domain.as_deref(), json),
    }
}

fn cmd_gap_rank(frontier_path: &Path, top: usize, domain: Option<&str>, json_output: bool) {
    let frontier = load_frontier_or_fail(frontier_path);
    let mut ranked = frontier
        .findings
        .iter()
        .filter(|finding| finding.flags.gap || finding.flags.negative_space)
        .filter(|finding| {
            domain.is_none_or(|domain| {
                finding
                    .assertion
                    .text
                    .to_lowercase()
                    .contains(&domain.to_lowercase())
                    || finding
                        .assertion
                        .entities
                        .iter()
                        .any(|entity| entity.name.to_lowercase().contains(&domain.to_lowercase()))
            })
        })
        .map(|finding| {
            let dependency_count = frontier
                .findings
                .iter()
                .flat_map(|candidate| candidate.links.iter())
                .filter(|link| link.target == finding.id)
                .count();
            let score = dependency_count as f64 + finding.confidence.score;
            json!({
                "id": &finding.id,
                "kind": "candidate_gap_review_lead",
                "assertion": &finding.assertion.text,
                "score": score,
                "dependency_count": dependency_count,
                "confidence": finding.confidence.score,
                "evidence_type": &finding.evidence.evidence_type,
                "entities": finding.assertion.entities.iter().map(|e| &e.name).collect::<Vec<_>>(),
                "recommended_action": "Review source scope and missing evidence before treating this as an experiment target.",
                "caveats": ["Candidate gap rankings are review leads, not guaranteed underexplored areas or experiment targets."],
            })
        })
        .collect::<Vec<_>>();
    ranked.sort_by(|a, b| {
        b.get("score")
            .and_then(Value::as_f64)
            .partial_cmp(&a.get("score").and_then(Value::as_f64))
            .unwrap_or(std::cmp::Ordering::Equal)
    });
    ranked.truncate(top);
    if json_output {
        let source_hash = hash_path_or_fail(frontier_path);
        let payload = json!({
            "ok": true,
            "command": "gaps rank",
            "schema_version": project::VELA_SCHEMA_VERSION,
            "frontier": {
                "name": &frontier.project.name,
                "source": frontier_path.display().to_string(),
                "hash": format!("sha256:{source_hash}"),
            },
            "filters": {
                "top": top,
                "domain": domain,
            },
            "count": ranked.len(),
            "ranking_label": "candidate gap review leads",
            "caveats": ["These rankings are navigation signals over flagged findings, not scientific conclusions."],
            "review_leads": ranked.clone(),
            "gaps": ranked,
        });
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize gap ranking")
        );
    } else {
        println!();
        println!("  {}", "CANDIDATE GAP REVIEW LEADS".dimmed());
        println!("  {}", style::tick_row(60));
        println!("  review source scope; these are not guaranteed experiment targets.");
        println!();
        for (idx, gap) in ranked.iter().enumerate() {
            println!(
                "  {}. [{}] score={} {}",
                idx + 1,
                gap["id"].as_str().unwrap_or("?"),
                gap["score"].as_f64().unwrap_or(0.0),
                gap["assertion"].as_str().unwrap_or("")
            );
        }
    }
}

async fn cmd_bridge(inputs: &[PathBuf], check_novelty: bool, top_n: usize) {
    if inputs.len() < 2 {
        fail("need at least 2 frontier files for bridge detection.");
    }
    println!();
    println!("  {}", "VELA · BRIDGE · V0.36.0".dimmed());
    println!("  {}", style::tick_row(60));
    println!("  loading {} frontiers...", inputs.len());
    let mut named_projects = Vec::<(String, project::Project)>::new();
    let mut total_findings = 0;
    for path in inputs {
        let frontier = load_frontier_or_fail(path);
        let name = path
            .file_stem()
            .unwrap_or_default()
            .to_string_lossy()
            .to_string();
        println!("  {} · {} findings", name, frontier.stats.findings);
        total_findings += frontier.stats.findings;
        named_projects.push((name, frontier));
    }
    let refs = named_projects
        .iter()
        .map(|(name, frontier)| (name.as_str(), frontier))
        .collect::<Vec<_>>();
    let mut bridges = bridge::detect_bridges(&refs);
    if check_novelty && !bridges.is_empty() {
        let client = Client::new();
        let check_count = bridges.len().min(top_n);
        println!("  running rough PubMed prior-art checks for top {check_count} bridges...");
        for bridge_item in bridges.iter_mut().take(check_count) {
            let query = bridge::novelty_query(&bridge_item.entity_name, bridge_item);
            match bridge::check_novelty(&client, &query).await {
                Ok(count) => bridge_item.pubmed_count = Some(count),
                Err(e) => eprintln!(
                    "  {} prior-art check failed for {}: {e}",
                    style::err_prefix(),
                    bridge_item.entity_name
                ),
            }
            tokio::time::sleep(std::time::Duration::from_millis(350)).await;
        }
    }
    print!("{}", bridge::format_report(&bridges, total_findings));
}

struct BenchArgs {
    frontier: Option<PathBuf>,
    gold: Option<PathBuf>,
    entity_gold: Option<PathBuf>,
    link_gold: Option<PathBuf>,
    suite: Option<PathBuf>,
    suite_ready: bool,
    min_f1: Option<f64>,
    min_precision: Option<f64>,
    min_recall: Option<f64>,
    no_thresholds: bool,
    json: bool,
}

/// v0.26 VelaBench: compare a candidate frontier (typically agent-
/// generated) against a gold frontier. Pure data comparison —
/// no LLM call, no network, deterministic. Exits non-zero when
/// the composite falls below `threshold` (default 0.0 = report only).
fn cmd_agent_bench(
    gold: &Path,
    candidate: &Path,
    sources: Option<&Path>,
    threshold: Option<f64>,
    report_path: Option<&Path>,
    json_out: bool,
) {
    let input = crate::agent_bench::BenchInput {
        gold_path: gold.to_path_buf(),
        candidate_path: candidate.to_path_buf(),
        sources: sources.map(Path::to_path_buf),
        threshold: threshold.unwrap_or(0.0),
    };
    let report = match crate::agent_bench::run(input) {
        Ok(r) => r,
        Err(e) => {
            eprintln!("{} bench failed: {e}", style::err_prefix());
            std::process::exit(1);
        }
    };

    let json = serde_json::to_string_pretty(&report).unwrap_or_default();
    if let Some(path) = report_path
        && let Err(e) = std::fs::write(path, &json)
    {
        eprintln!(
            "{} failed to write report to {}: {e}",
            style::err_prefix(),
            path.display()
        );
    }

    if json_out {
        println!("{json}");
    } else {
        println!();
        println!("  {}", "VELA · BENCH · AGENT STATE-UPDATE".dimmed());
        println!("  {}", style::tick_row(60));
        print!("{}", crate::agent_bench::render_pretty(&report));
        println!();
    }

    if !report.pass {
        std::process::exit(1);
    }
}

fn cmd_bench(args: BenchArgs) {
    if args.suite_ready {
        let suite_path = args
            .suite
            .unwrap_or_else(|| PathBuf::from("benchmarks/suites/bbb-core.json"));
        let payload =
            benchmark::suite_ready_report(&suite_path).unwrap_or_else(|e| fail_return(&e));
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize suite-ready report")
        );
        if payload.get("ok").and_then(Value::as_bool) != Some(true) {
            std::process::exit(1);
        }
        return;
    }
    if let Some(suite_path) = args.suite {
        let payload = benchmark::run_suite(&suite_path).unwrap_or_else(|e| fail_return(&e));
        if args.json {
            println!(
                "{}",
                serde_json::to_string_pretty(&payload)
                    .expect("failed to serialize benchmark suite")
            );
        } else {
            let ok = payload.get("ok").and_then(Value::as_bool) == Some(true);
            let metrics = payload.get("metrics").unwrap_or(&Value::Null);
            println!();
            println!("  {}", "VELA · BENCH · SUITE".dimmed());
            println!("  {}", style::tick_row(60));
            println!("  suite: {}", suite_path.display());
            println!(
                "  status: {}",
                if ok {
                    style::ok("pass")
                } else {
                    style::lost("fail")
                }
            );
            println!(
                "  tasks: {}/{} passed",
                metrics
                    .get("tasks_passed")
                    .and_then(Value::as_u64)
                    .unwrap_or(0),
                metrics
                    .get("tasks_total")
                    .and_then(Value::as_u64)
                    .unwrap_or(0)
            );
        }
        if payload.get("ok").and_then(Value::as_bool) != Some(true) {
            std::process::exit(1);
        }
        return;
    }

    let frontier = args
        .frontier
        .unwrap_or_else(|| PathBuf::from("frontiers/bbb-alzheimer.json"));
    let thresholds = benchmark::BenchmarkThresholds {
        min_f1: if args.no_thresholds {
            None
        } else {
            args.min_f1.or(Some(0.05))
        },
        min_precision: if args.no_thresholds {
            None
        } else {
            args.min_precision
        },
        min_recall: if args.no_thresholds {
            None
        } else {
            args.min_recall
        },
        ..Default::default()
    };
    if let Some(path) = args.link_gold {
        print_benchmark_or_exit(benchmark::task_envelope(
            &frontier,
            None,
            benchmark::BenchmarkMode::Link,
            Some(&path),
            &thresholds,
            None,
        ));
    } else if let Some(path) = args.entity_gold {
        print_benchmark_or_exit(benchmark::task_envelope(
            &frontier,
            None,
            benchmark::BenchmarkMode::Entity,
            Some(&path),
            &thresholds,
            None,
        ));
    } else if let Some(path) = args.gold {
        if args.json {
            print_benchmark_or_exit(benchmark::task_envelope(
                &frontier,
                None,
                benchmark::BenchmarkMode::Finding,
                Some(&path),
                &thresholds,
                None,
            ));
        } else {
            benchmark::run(&frontier, &path, false);
        }
    } else {
        fail("Provide --suite, --gold, --entity-gold, or --link-gold.");
    }
}

fn print_benchmark_or_exit(result: Result<Value, String>) {
    let payload = result.unwrap_or_else(|e| fail_return(&e));
    println!(
        "{}",
        serde_json::to_string_pretty(&payload).expect("failed to serialize benchmark report")
    );
    if payload.get("ok").and_then(Value::as_bool) != Some(true) {
        std::process::exit(1);
    }
}

fn cmd_packet(action: PacketAction) {
    let (result, json_output) = match action {
        PacketAction::Inspect { path, json } => (packet::inspect(&path), json),
        PacketAction::Validate { path, json } => (packet::validate(&path), json),
    };
    match result {
        Ok(output) if json_output => {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "ok": true,
                    "command": "packet",
                    "result": output,
                }))
                .expect("failed to serialize packet response")
            );
        }
        Ok(output) => println!("{output}"),
        Err(e) => fail(&e),
    }
}

/// `vela verify <packet_dir>` — same code path as
/// `vela packet validate`, surfaced under a friendlier top-level name.
/// Reads every file in the manifest, recomputes SHA-256, validates the
/// proof-trace chain. Exit 0 on all-match, 1 on any mismatch.
fn cmd_verify(path: &Path, json_output: bool) {
    let result = packet::validate(path);
    match result {
        Ok(output) if json_output => {
            println!(
                "{}",
                serde_json::to_string_pretty(&json!({
                    "ok": true,
                    "command": "verify",
                    "result": output,
                }))
                .expect("failed to serialize verify response")
            );
        }
        Ok(output) => {
            println!("{output}");
            println!(
                "\nverify: ok\n  every file in the manifest matched its claimed sha256.\n  pull this packet on another machine, run the same command, see the same line."
            );
        }
        Err(e) => fail(&e),
    }
}

fn cmd_init(path: &Path, name: &str, template: &str, initialize_git: bool, json_output: bool) {
    if path.join(".vela").exists() {
        fail(&format!(
            "already initialized: {} exists",
            path.join(".vela").display()
        ));
    }
    let payload = frontier_repo::initialize(
        path,
        frontier_repo::InitOptions {
            name,
            template,
            initialize_git,
        },
    )
    .unwrap_or_else(|e| fail_return(&e));
    if json_output {
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize init report")
        );
    } else {
        println!(
            "{} initialized frontier repository in {}",
            style::ok("ok"),
            path.display()
        );
    }
}

/// v0.103: end-to-end first-run wizard. Composes `vela init`, `vela
/// sign generate-keypair`, `vela actor add`, and `vela finding add
/// --apply` into a single command. Each step shells out to the
/// current binary so the wizard's behavior matches running the
/// commands directly. Failure of any step aborts; partial state is
/// left on disk for the user to inspect.
fn cmd_quickstart(
    path: &Path,
    name: &str,
    reviewer: &str,
    assertion: Option<&str>,
    keys_out: Option<&Path>,
    json_output: bool,
) {
    use std::process::Command;

    if path.join(".vela").exists() {
        fail(&format!(
            "already initialized: {} exists",
            path.join(".vela").display()
        ));
    }

    let exe = std::env::current_exe()
        .unwrap_or_else(|e| fail_return(&format!("cannot locate current executable: {e}")));
    let keys_dir = keys_out
        .map(Path::to_path_buf)
        .unwrap_or_else(|| path.join("keys"));
    let assertion_text =
        assertion.unwrap_or("Quickstart placeholder claim. Replace with your real assertion.");

    let run_step = |label: &str, args: &[&str]| -> std::process::Output {
        let out = Command::new(&exe)
            .args(args)
            .output()
            .unwrap_or_else(|e| fail_return(&format!("{label}: failed to spawn: {e}")));
        if !out.status.success() {
            let stderr = String::from_utf8_lossy(&out.stderr);
            fail(&format!("{label} failed:\n{stderr}"));
        }
        out
    };

    // Step 1: init the frontier.
    run_step(
        "init",
        &[
            "init",
            path.to_string_lossy().as_ref(),
            "--name",
            name,
            "--no-git",
            "--json",
        ],
    );

    // Step 2: generate keypair.
    let keys_out_str = keys_dir.to_string_lossy().into_owned();
    let keypair_out = run_step(
        "sign.generate-keypair",
        &[
            "sign",
            "generate-keypair",
            "--out",
            keys_out_str.as_ref(),
            "--json",
        ],
    );
    let keypair_json: serde_json::Value = serde_json::from_slice(&keypair_out.stdout)
        .unwrap_or_else(|e| fail_return(&format!("sign.generate-keypair: bad json: {e}")));
    let public_key = keypair_json
        .get("public_key")
        .and_then(|v| v.as_str())
        .unwrap_or_else(|| fail_return("sign.generate-keypair: missing public_key in output"))
        .to_string();

    // Step 3: register the reviewer actor.
    run_step(
        "actor.add",
        &[
            "actor",
            "add",
            path.to_string_lossy().as_ref(),
            reviewer,
            "--pubkey",
            public_key.as_str(),
            "--json",
        ],
    );

    // Step 4: add and apply the first finding.
    let finding_out = run_step(
        "finding.add",
        &[
            "finding",
            "add",
            path.to_string_lossy().as_ref(),
            "--assertion",
            assertion_text,
            "--author",
            reviewer,
            "--apply",
            "--json",
        ],
    );
    let finding_json: serde_json::Value = serde_json::from_slice(&finding_out.stdout)
        .unwrap_or_else(|e| fail_return(&format!("finding.add: bad json: {e}")));
    let finding_id = finding_json
        .get("finding_id")
        .and_then(|v| v.as_str())
        .map(str::to_string);

    if json_output {
        let payload = json!({
            "ok": true,
            "command": "quickstart",
            "frontier": path.display().to_string(),
            "name": name,
            "reviewer": reviewer,
            "public_key": public_key,
            "keys_dir": keys_dir.display().to_string(),
            "finding_id": finding_id,
            "next_steps": [
                format!("vela serve {}", path.display()),
                format!(
                    "vela ingest <paper.pdf|doi:...> --frontier {}",
                    path.display()
                ),
                format!("vela log {}", path.display()),
            ],
        });
        println!(
            "{}",
            serde_json::to_string_pretty(&payload).expect("failed to serialize quickstart")
        );
        return;
    }

    println!();
    println!(
        "  {}",
        format!("VELA · QUICKSTART · {}", path.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    println!("  frontier:  {}", path.display());
    println!("  name:      {name}");
    println!("  reviewer:  {reviewer}");
    println!("  keys:      {}", keys_dir.display());
    println!("  pubkey:    {}…", &public_key[..16]);
    if let Some(id) = finding_id.as_deref() {
        println!("  finding:   {id}");
    }
    println!();
    println!("  {}", style::ok("done"));
    println!("  next:");
    println!("    vela serve {}", path.display());
    println!(
        "    vela ingest <paper.pdf|doi:10.xxx|pmid:xxx> --frontier {}",
        path.display()
    );
    println!("    vela log {}", path.display());
    println!();
}

/// v0.109: regenerate or verify the frontier's vela.lock.
/// Default mode runs `frontier_repo::materialize` which rebuilds
/// the lock from current state. `--check` reads the existing
/// lock and verifies on-disk hashes match the recorded values
/// without writing anything; exits 1 on drift.
fn cmd_lock(path: &Path, check: bool, json_output: bool) {
    if check {
        cmd_lock_check(path, json_output);
        return;
    }
    let payload = crate::frontier_repo::materialize(path).unwrap_or_else(|e| fail_return(&e));
    if json_output {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": true,
                "command": "lock",
                "path": path.display().to_string(),
                "snapshot_hash": payload.get("snapshot_hash"),
                "event_log_hash": payload.get("event_log_hash"),
                "proposal_state_hash": payload.get("proposal_state_hash"),
            }))
            .expect("failed to serialize lock report")
        );
        return;
    }
    println!();
    println!(
        "  {}",
        format!("VELA · LOCK · {}", path.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    println!(
        "  snapshot_hash:        {}",
        payload
            .get("snapshot_hash")
            .and_then(|v| v.as_str())
            .unwrap_or("?")
    );
    println!(
        "  event_log_hash:       {}",
        payload
            .get("event_log_hash")
            .and_then(|v| v.as_str())
            .unwrap_or("?")
    );
    println!(
        "  proposal_state_hash:  {}",
        payload
            .get("proposal_state_hash")
            .and_then(|v| v.as_str())
            .unwrap_or("?")
    );
    println!();
    println!("  {}", style::ok("locked"));
}

fn cmd_lock_check(path: &Path, json_output: bool) {
    use crate::frontier_repo::read_lock;
    let lock = read_lock(path).unwrap_or_else(|e| fail_return(&e));
    let Some(lock) = lock else {
        fail("lock --check: no vela.lock found at path");
    };
    let project = repo::load_from_path(path).unwrap_or_else(|e| fail_return(&e));
    let current_snapshot = format!("sha256:{}", crate::events::snapshot_hash(&project));
    let current_event_log = format!("sha256:{}", crate::events::event_log_hash(&project.events));
    let mut drift: Vec<String> = Vec::new();
    if lock.snapshot_hash != current_snapshot {
        drift.push(format!(
            "snapshot_hash: lock={} current={}",
            lock.snapshot_hash, current_snapshot
        ));
    }
    if lock.event_log_hash != current_event_log {
        drift.push(format!(
            "event_log_hash: lock={} current={}",
            lock.event_log_hash, current_event_log
        ));
    }
    let ok = drift.is_empty();
    if json_output {
        println!(
            "{}",
            serde_json::to_string_pretty(&json!({
                "ok": ok,
                "command": "lock.check",
                "path": path.display().to_string(),
                "drift": drift,
                "lock_snapshot_hash": lock.snapshot_hash,
                "current_snapshot_hash": current_snapshot,
                "lock_event_log_hash": lock.event_log_hash,
                "current_event_log_hash": current_event_log,
                "dependency_count": lock.dependencies.len(),
            }))
            .expect("failed to serialize lock check report")
        );
    } else {
        println!();
        println!(
            "  {}",
            format!("VELA · LOCK · CHECK · {}", path.display())
                .to_uppercase()
                .dimmed()
        );
        println!("  {}", style::tick_row(60));
        if ok {
            println!("  snapshot_hash:        {}", lock.snapshot_hash);
            println!("  event_log_hash:       {}", lock.event_log_hash);
            println!("  dependencies pinned:  {}", lock.dependencies.len());
            println!();
            println!("  {} on-disk state matches vela.lock", style::ok("ok"));
        } else {
            println!("  {} drift detected:", style::err_prefix());
            for d in &drift {
                println!("    - {d}");
            }
        }
    }
    if !ok {
        std::process::exit(1);
    }
}

/// v0.110: write a static HTML documentation site for the
/// frontier at `path`. Output lands in `<path>/doc/` by default
/// or in the user-supplied `--out` directory. Cargo's docs.rs
/// analog for scientific state.
fn cmd_doc(path: &Path, out: Option<&Path>, json_output: bool) {
    let project = repo::load_from_path(path).unwrap_or_else(|e| fail_return(&e));
    let out_dir = out
        .map(Path::to_path_buf)
        .unwrap_or_else(|| path.join("doc"));
    let report =
        crate::doc_render::write_site(&project, &out_dir).unwrap_or_else(|e| fail_return(&e));
    if json_output {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("failed to serialize doc report")
        );
        return;
    }
    println!();
    println!(
        "  {}",
        format!("VELA · DOC · {}", path.display())
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    println!("  frontier_id:        {}", report.frontier_id);
    println!("  out:                {}", report.out);
    println!("  files written:      {}", report.files_written);
    println!("  findings:           {}", report.findings_documented);
    println!("  events:             {}", report.events_documented);
    println!();
    println!(
        "  {} open {}/index.html in a browser",
        style::ok("ok"),
        report.out
    );
}

fn cmd_import(frontier_path: &Path, into: Option<&Path>) {
    let frontier = repo::load_from_path(frontier_path).unwrap_or_else(|e| fail_return(&e));
    let target = into
        .map(Path::to_path_buf)
        .unwrap_or_else(|| PathBuf::from(frontier.project.name.replace(' ', "-").to_lowercase()));
    repo::init_repo(&target, &frontier).unwrap_or_else(|e| fail(&e));
    println!(
        "{} {} findings · {}",
        style::ok("imported"),
        frontier.findings.len(),
        target.display()
    );
}

fn cmd_locator_repair(
    path: &Path,
    atom_id: &str,
    locator_override: Option<&str>,
    reviewer: &str,
    reason: &str,
    apply: bool,
    json_output: bool,
) {
    let report = state::repair_evidence_atom_locator(
        path,
        atom_id,
        locator_override,
        reviewer,
        reason,
        apply,
    )
    .unwrap_or_else(|e| fail_return(&e));
    print_state_report(&report, json_output);
}

/// v0.57: Fetch metadata + abstract for an external source.
/// Cache-first: if a cache hit exists and `--refresh` was not
/// passed, return the cached JSON. Otherwise call the right
/// upstream (Crossref / NCBI eutils / ClinicalTrials.gov v2).
async fn cmd_source_fetch(
    identifier: &str,
    cache_root: Option<&Path>,
    out_path: Option<&Path>,
    refresh: bool,
    _json_output: bool,
) {
    use sha2::{Digest, Sha256};

    let normalized = normalize_source_identifier(identifier);
    let cache_path = cache_root.map(|root| {
        let hash = format!("{:x}", Sha256::digest(normalized.as_bytes()));
        root.join("sources")
            .join("cache")
            .join(format!("{hash}.json"))
    });

    if !refresh
        && let Some(p) = cache_path.as_ref()
        && p.is_file()
    {
        let body = std::fs::read_to_string(p)
            .unwrap_or_else(|e| fail_return(&format!("read cache {}: {e}", p.display())));
        emit_source_fetch_result(&body, out_path);
        return;
    }

    let result = fetch_source_metadata(&normalized).await;
    let json = match result {
        Ok(value) => serde_json::to_string_pretty(&value)
            .unwrap_or_else(|e| fail_return(&format!("serialize fetched record: {e}"))),
        Err(e) => fail_return(&format!("source-fetch '{identifier}': {e}")),
    };

    if let Some(p) = cache_path.as_ref() {
        if let Some(parent) = p.parent() {
            std::fs::create_dir_all(parent)
                .unwrap_or_else(|e| fail_return(&format!("mkdir {}: {e}", parent.display())));
        }
        std::fs::write(p, &json)
            .unwrap_or_else(|e| fail_return(&format!("write cache {}: {e}", p.display())));
    }
    emit_source_fetch_result(&json, out_path);
}

fn emit_source_fetch_result(body: &str, out_path: Option<&Path>) {
    if let Some(p) = out_path {
        if let Some(parent) = p.parent() {
            let _ = std::fs::create_dir_all(parent);
        }
        std::fs::write(p, body)
            .unwrap_or_else(|e| fail_return(&format!("write {}: {e}", p.display())));
    } else {
        println!("{body}");
    }
}

fn normalize_source_identifier(raw: &str) -> String {
    let trimmed = raw.trim();
    if trimmed.starts_with("doi:")
        || trimmed.starts_with("pmid:")
        || trimmed.starts_with("nct:")
        || trimmed.starts_with("pmc:")
    {
        return trimmed.to_string();
    }
    if trimmed.starts_with("10.") {
        return format!("doi:{trimmed}");
    }
    if trimmed.starts_with("NCT") || trimmed.starts_with("nct") {
        return format!(
            "nct:{}",
            trimmed
                .to_uppercase()
                .trim_start_matches("NCT")
                .to_string()
                .split_at(0)
                .0
        );
    }
    if trimmed.chars().all(|c| c.is_ascii_digit()) {
        return format!("pmid:{trimmed}");
    }
    trimmed.to_string()
}

async fn fetch_source_metadata(normalized: &str) -> Result<Value, String> {
    let client = Client::builder()
        .user_agent("vela/0.66.0 (vela-source-fetch; +https://vela-science.fly.dev)")
        .timeout(std::time::Duration::from_secs(30))
        .build()
        .map_err(|e| format!("client build: {e}"))?;
    if let Some(rest) = normalized.strip_prefix("doi:") {
        // v0.66: DOI primary path is Crossref. If Crossref returns
        // an empty abstract (common for NEJM, JAMA, gated journals),
        // fall through to a PubMed lookup via DOI -> PMID and merge
        // the abstract back into the Crossref record. Keeps Crossref
        // metadata (title, year, journal, authors) authoritative;
        // only fills the abstract gap.
        let mut record = fetch_via_crossref(&client, rest).await?;
        let crossref_abstract = record
            .get("abstract")
            .and_then(|v| v.as_str())
            .unwrap_or("");
        if crossref_abstract.is_empty()
            && let Some(pmid) = resolve_doi_to_pmid(&client, rest).await
            && let Ok(pubmed_record) = fetch_via_pubmed(&client, &pmid).await
        {
            let pubmed_abstract = pubmed_record
                .get("abstract")
                .and_then(|v| v.as_str())
                .unwrap_or("")
                .to_string();
            if !pubmed_abstract.is_empty()
                && let Some(obj) = record.as_object_mut()
            {
                obj.insert("abstract".to_string(), Value::String(pubmed_abstract));
                obj.insert(
                    "abstract_source".to_string(),
                    Value::String(format!("pubmed:{pmid}")),
                );
            }
        }
        return Ok(record);
    }
    if let Some(rest) = normalized.strip_prefix("pmid:") {
        return fetch_via_pubmed(&client, rest).await;
    }
    if let Some(rest) = normalized.strip_prefix("nct:") {
        return fetch_via_ctgov(&client, rest).await;
    }
    Err(format!(
        "unsupported source identifier '{normalized}'. Use doi:, pmid:, or nct: prefix."
    ))
}

/// v0.66: resolve a DOI to a PubMed PMID via eutils esearch. Returns
/// None if no PMID is found or the lookup fails. The abstract-fallback
/// path uses this to enrich Crossref records that have empty abstracts.
async fn resolve_doi_to_pmid(client: &Client, doi: &str) -> Option<String> {
    let url = format!(
        "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term={}[doi]&retmode=json",
        urlencoding::encode(doi)
    );
    let resp = client.get(&url).send().await.ok()?;
    if !resp.status().is_success() {
        return None;
    }
    let body: Value = resp.json().await.ok()?;
    let id_list = body.pointer("/esearchresult/idlist")?.as_array()?;
    if id_list.len() != 1 {
        // Refuse ambiguous matches; the substrate would rather have
        // an empty abstract than the wrong paper's text.
        return None;
    }
    id_list.first()?.as_str().map(|s| s.to_string())
}

async fn fetch_via_crossref(client: &Client, doi: &str) -> Result<Value, String> {
    let url = format!("https://api.crossref.org/works/{doi}");
    let resp = client
        .get(&url)
        .send()
        .await
        .map_err(|e| format!("crossref get: {e}"))?;
    if !resp.status().is_success() {
        return Err(format!("crossref returned {}", resp.status()));
    }
    let body: Value = resp
        .json()
        .await
        .map_err(|e| format!("crossref json: {e}"))?;
    let work = body.get("message").cloned().unwrap_or(Value::Null);
    let title = work
        .get("title")
        .and_then(|v| v.as_array())
        .and_then(|a| a.first())
        .and_then(|v| v.as_str())
        .unwrap_or("")
        .to_string();
    let abstract_html = work
        .get("abstract")
        .and_then(|v| v.as_str())
        .unwrap_or("")
        .to_string();
    let abstract_text = strip_jats_tags(&abstract_html);
    let year = work
        .get("issued")
        .and_then(|v| v.get("date-parts"))
        .and_then(|v| v.as_array())
        .and_then(|a| a.first())
        .and_then(|v| v.as_array())
        .and_then(|a| a.first())
        .and_then(|v| v.as_i64());
    let journal = work
        .get("container-title")
        .and_then(|v| v.as_array())
        .and_then(|a| a.first())
        .and_then(|v| v.as_str())
        .unwrap_or("")
        .to_string();
    let authors = work
        .get("author")
        .and_then(|v| v.as_array())
        .map(|arr| {
            arr.iter()
                .filter_map(|a| {
                    let given = a.get("given").and_then(|v| v.as_str()).unwrap_or("");
                    let family = a.get("family").and_then(|v| v.as_str()).unwrap_or("");
                    let combined = format!("{given} {family}").trim().to_string();
                    if combined.is_empty() {
                        None
                    } else {
                        Some(combined)
                    }
                })
                .collect::<Vec<_>>()
        })
        .unwrap_or_default();
    Ok(json!({
        "schema": "vela.source_fetch.v0.1",
        "identifier": format!("doi:{doi}"),
        "source": "crossref",
        "title": title,
        "abstract": abstract_text,
        "year": year,
        "journal": journal,
        "authors": authors,
        "retrieved_at": chrono::Utc::now().to_rfc3339(),
    }))
}

async fn fetch_via_pubmed(client: &Client, pmid: &str) -> Result<Value, String> {
    let url = format!(
        "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={pmid}&retmode=xml"
    );
    let resp = client
        .get(&url)
        .send()
        .await
        .map_err(|e| format!("pubmed get: {e}"))?;
    if !resp.status().is_success() {
        return Err(format!("pubmed returned {}", resp.status()));
    }
    let xml = resp.text().await.map_err(|e| format!("pubmed text: {e}"))?;
    let title = extract_xml_text(&xml, "<ArticleTitle>", "</ArticleTitle>");
    let abstract_text = extract_xml_text(&xml, "<AbstractText>", "</AbstractText>");
    let year = extract_xml_text(&xml, "<Year>", "</Year>")
        .parse::<i64>()
        .ok();
    let journal = extract_xml_text(&xml, "<Title>", "</Title>");
    Ok(json!({
        "schema": "vela.source_fetch.v0.1",
        "identifier": format!("pmid:{pmid}"),
        "source": "pubmed",
        "title": title,
        "abstract": abstract_text,
        "year": year,
        "journal": journal,
        "authors": Vec::<String>::new(),
        "retrieved_at": chrono::Utc::now().to_rfc3339(),
    }))
}

async fn fetch_via_ctgov(client: &Client, nct: &str) -> Result<Value, String> {
    let nct_clean = nct.trim();
    let nct_id = if nct_clean.starts_with("NCT") || nct_clean.starts_with("nct") {
        nct_clean.to_uppercase()
    } else {
        format!("NCT{nct_clean}")
    };
    let url = format!("https://clinicaltrials.gov/api/v2/studies/{nct_id}");
    let resp = client
        .get(&url)
        .send()
        .await
        .map_err(|e| format!("ctgov get: {e}"))?;
    if !resp.status().is_success() {
        return Err(format!("ctgov returned {}", resp.status()));
    }
    let body: Value = resp.json().await.map_err(|e| format!("ctgov json: {e}"))?;
    let title = body
        .pointer("/protocolSection/identificationModule/briefTitle")
        .and_then(|v| v.as_str())
        .unwrap_or("")
        .to_string();
    let abstract_text = body
        .pointer("/protocolSection/descriptionModule/briefSummary")
        .and_then(|v| v.as_str())
        .unwrap_or("")
        .to_string();
    let phase = body
        .pointer("/protocolSection/designModule/phases")
        .and_then(|v| v.as_array())
        .and_then(|a| a.first())
        .and_then(|v| v.as_str())
        .unwrap_or("")
        .to_string();
    Ok(json!({
        "schema": "vela.source_fetch.v0.1",
        "identifier": format!("nct:{nct_id}"),
        "source": "clinicaltrials.gov",
        "title": title,
        "abstract": abstract_text,
        "year": Value::Null,
        "journal": phase,
        "authors": Vec::<String>::new(),
        "retrieved_at": chrono::Utc::now().to_rfc3339(),
    }))
}

fn extract_xml_text(xml: &str, open: &str, close: &str) -> String {
    if let Some(start) = xml.find(open) {
        let after = &xml[start + open.len()..];
        if let Some(end) = after.find(close) {
            return after[..end].trim().to_string();
        }
    }
    String::new()
}

fn strip_jats_tags(html: &str) -> String {
    let mut out = String::with_capacity(html.len());
    let mut in_tag = false;
    for c in html.chars() {
        match c {
            '<' => in_tag = true,
            '>' => in_tag = false,
            _ if !in_tag => out.push(c),
            _ => {}
        }
    }
    out.split_whitespace().collect::<Vec<_>>().join(" ")
}

fn cmd_span_repair(
    path: &Path,
    finding_id: &str,
    section: &str,
    text: &str,
    reviewer: &str,
    reason: &str,
    apply: bool,
    json_output: bool,
) {
    let report =
        state::repair_finding_span(path, finding_id, section, text, reviewer, reason, apply)
            .unwrap_or_else(|e| fail_return(&e));
    print_state_report(&report, json_output);
}

#[allow(clippy::too_many_arguments)]
fn cmd_entity_resolve(
    path: &Path,
    finding_id: &str,
    entity_name: &str,
    source: &str,
    id: &str,
    confidence: f64,
    matched_name: Option<&str>,
    resolution_method: &str,
    reviewer: &str,
    reason: &str,
    apply: bool,
    json_output: bool,
) {
    let report = state::resolve_finding_entity(
        path,
        finding_id,
        entity_name,
        source,
        id,
        confidence,
        matched_name,
        resolution_method,
        reviewer,
        reason,
        apply,
    )
    .unwrap_or_else(|e| fail_return(&e));
    print_state_report(&report, json_output);
}

fn cmd_propagate(
    path: &Path,
    retract: Option<String>,
    reduce_confidence: Option<String>,
    to: Option<f64>,
    output: Option<&Path>,
) {
    let mut frontier = load_frontier_or_fail(path);
    let (finding_id, action, label) = if let Some(id) = retract {
        (id, propagate::PropagationAction::Retracted, "retraction")
    } else if let Some(id) = reduce_confidence {
        let score = to.unwrap_or_else(|| fail_return("--reduce-confidence requires --to <score>"));
        if !(0.0..=1.0).contains(&score) {
            fail("--to must be between 0.0 and 1.0");
        }
        (
            id,
            propagate::PropagationAction::ConfidenceReduced { new_score: score },
            "confidence reduction",
        )
    } else {
        fail("specify --retract <id> or --reduce-confidence <id> --to <score>");
    };
    if !frontier.findings.iter().any(|f| f.id == finding_id) {
        fail(&format!("finding not found: {finding_id}"));
    }
    let result = propagate::propagate_correction(&mut frontier, &finding_id, action);
    // v0.36.2: persist propagation events into the canonical review
    // log. Pre-v0.36.2 these were emitted to stdout and lost — the
    // kernel forgot why a finding was flagged the moment the command
    // returned.
    frontier.review_events.extend(result.events.clone());
    project::recompute_stats(&mut frontier);
    propagate::print_result(&result, label, &finding_id);
    let out = output.unwrap_or(path);
    repo::save_to_path(out, &frontier).expect("Failed to save frontier");
    println!("  output: {}", out.display());
}

fn cmd_mcp_setup(source: Option<&Path>, frontiers: Option<&Path>) {
    let source_desc = source
        .map(|p| p.display().to_string())
        .or_else(|| frontiers.map(|p| p.display().to_string()))
        .unwrap_or_else(|| "frontier.json".to_string());
    let args = if let Some(path) = source {
        format!(r#""serve", "{}""#, path.display())
    } else if let Some(path) = frontiers {
        format!(r#""serve", "--frontiers", "{}""#, path.display())
    } else {
        r#""serve", "frontier.json""#.to_string()
    };
    println!(
        r#"Add this MCP server configuration to your client:

{{
  "mcpServers": {{
    "vela": {{
      "command": "vela",
      "args": [{args}]
    }}
  }}
}}

Source: {source_desc}"#
    );
}

fn parse_entities(input: &str) -> Vec<(String, String)> {
    if input.trim().is_empty() {
        return Vec::new();
    }
    input
        .split(',')
        .filter_map(|pair| {
            let parts = pair.trim().splitn(2, ':').collect::<Vec<_>>();
            if parts.len() == 2 {
                Some((parts[0].trim().to_string(), parts[1].trim().to_string()))
            } else {
                eprintln!(
                    "{} skipping malformed entity '{}'",
                    style::warn("warn"),
                    pair.trim()
                );
                None
            }
        })
        .collect()
}

fn parse_evidence_spans(inputs: &[String]) -> Vec<Value> {
    inputs
        .iter()
        .filter_map(|input| {
            let trimmed = input.trim();
            if trimmed.is_empty() {
                return None;
            }
            if trimmed.starts_with('{') {
                match serde_json::from_str::<Value>(trimmed) {
                    Ok(value @ Value::Object(_)) => return Some(value),
                    Ok(_) | Err(_) => {
                        eprintln!(
                            "{} evidence span JSON should be an object; storing as text",
                            style::warn("warn")
                        );
                    }
                }
            }
            Some(json!({
                "section": "curator_source",
                "text": trimmed,
            }))
        })
        .collect()
}

fn hash_path(path: &Path) -> Result<String, String> {
    let mut hasher = Sha256::new();
    if path.is_file() {
        let bytes = std::fs::read(path)
            .map_err(|e| format!("Failed to read {} for hashing: {e}", path.display()))?;
        hasher.update(&bytes);
    } else if path.is_dir() {
        let mut files = Vec::new();
        collect_hash_files(path, path, &mut files)?;
        files.sort();
        for rel in files {
            hasher.update(rel.to_string_lossy().as_bytes());
            let bytes = std::fs::read(path.join(&rel))
                .map_err(|e| format!("Failed to read {} for hashing: {e}", rel.display()))?;
            hasher.update(bytes);
        }
    } else {
        return Err(format!("Cannot hash missing path {}", path.display()));
    }
    Ok(format!("{:x}", hasher.finalize()))
}

fn load_frontier_or_fail(path: &Path) -> project::Project {
    repo::load_from_path(path).unwrap_or_else(|e| {
        fail_return(&format!(
            "Failed to load frontier '{}': {e}",
            path.display()
        ))
    })
}

fn hash_path_or_fail(path: &Path) -> String {
    hash_path(path).unwrap_or_else(|e| {
        fail_return(&format!(
            "Failed to hash frontier '{}': {e}",
            path.display()
        ))
    })
}

fn collect_hash_files(root: &Path, dir: &Path, files: &mut Vec<PathBuf>) -> Result<(), String> {
    for entry in
        std::fs::read_dir(dir).map_err(|e| format!("Failed to read {}: {e}", dir.display()))?
    {
        let entry = entry.map_err(|e| format!("Failed to read directory entry: {e}"))?;
        let path = entry.path();
        if path.is_dir() {
            collect_hash_files(root, &path, files)?;
        } else if path.is_file() {
            files.push(
                path.strip_prefix(root)
                    .map_err(|e| e.to_string())?
                    .to_path_buf(),
            );
        }
    }
    Ok(())
}

fn schema_error_suggestion(error: &str) -> &'static str {
    if schema_error_action(error).is_some() {
        "Run `vela normalize` to repair deterministic frontier state."
    } else {
        "Inspect and correct the referenced frontier field."
    }
}

fn schema_error_fix(error: &str) -> bool {
    schema_error_action(error).is_some()
}

fn schema_error_action(error: &str) -> Option<&'static str> {
    if error.contains("stats.findings")
        || error.contains("stats.links")
        || error.contains("Invalid compiler")
        || error.contains("Invalid vela_version")
        || error.contains("Invalid schema")
    {
        Some("normalize_metadata_and_stats")
    } else if error.contains("does not match content-address") {
        Some("rewrite_ids")
    } else {
        None
    }
}

fn build_repair_plan(diagnostics: &[Value]) -> Vec<Value> {
    let mut actions = std::collections::BTreeMap::<String, usize>::new();
    for diagnostic in diagnostics {
        if let Some(action) = diagnostic.get("normalize_action").and_then(Value::as_str) {
            *actions.entry(action.to_string()).or_default() += 1;
        }
    }
    actions
        .into_iter()
        .map(|(action, count)| {
            let command = if action == "rewrite_ids" {
                "vela normalize <frontier> --write --rewrite-ids --id-map id-map.json"
            } else {
                "vela normalize <frontier> --write"
            };
            json!({
                "action": action,
                "count": count,
                "command": command,
            })
        })
        .collect()
}

fn cmd_integrity(frontier: &Path, json: bool) {
    let report = state_integrity::analyze_path(frontier).unwrap_or_else(|e| fail_return(&e));
    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("failed to serialize integrity report")
        );
    } else {
        println!("vela integrity");
        println!("  frontier: {}", frontier.display());
        println!("  status: {}", report.status);
        println!("  proof freshness: {}", report.proof_freshness);
        println!("  structural errors: {}", report.structural_errors.len());
        for error in report.structural_errors.iter().take(8) {
            println!("  - {}: {}", error.rule_id, error.message);
        }
    }
}

fn cmd_impact(frontier: &Path, finding_id: &str, depth: Option<usize>, json: bool) {
    let report =
        impact::analyze_path(frontier, finding_id, depth).unwrap_or_else(|e| fail_return(&e));
    if json {
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("failed to serialize impact report")
        );
    } else {
        println!("vela impact");
        println!("  finding: {}", report.target.id);
        println!("  frontier: {}", report.frontier.vfr_id);
        println!("  direct dependents: {}", report.summary.direct_dependents);
        println!("  downstream: {}", report.summary.total_downstream);
        println!("  open proposals: {}", report.summary.open_proposals);
        println!("  accepted events: {}", report.summary.accepted_events);
        println!("  proof: {}", report.summary.proof_status);
    }
}

fn cmd_discord(frontier: &Path, json: bool, kind_filter: Option<&str>) {
    use crate::discord::DiscordKind;
    use crate::discord_compute::compute_discord_assignment;

    let project = repo::load_from_path(frontier).unwrap_or_else(|e| fail_return(&e));
    let assignment = compute_discord_assignment(&project);
    let support = assignment.frontier_support();

    // Build the per-finding rows: only those with non-empty discord
    // (i.e. those in support), filtered by kind if requested.
    let mut rows: Vec<(String, Vec<String>)> = Vec::new();
    for context in support.iter() {
        let set = assignment.get(context);
        let kinds: Vec<String> = set.iter().map(|k| k.as_str().to_string()).collect();
        if let Some(filter) = kind_filter
            && !kinds.iter().any(|k| k == filter)
        {
            continue;
        }
        rows.push((context.clone(), kinds));
    }

    // Per-kind histogram across the full assignment (independent of
    // the row filter, so the histogram reflects the substrate's real
    // discord landscape).
    let mut histogram: std::collections::BTreeMap<&'static str, usize> =
        std::collections::BTreeMap::new();
    for kind in DiscordKind::ALL {
        let count = assignment
            .iter()
            .filter(|(_, set)| set.contains(*kind))
            .count();
        if count > 0 {
            histogram.insert(kind.as_str(), count);
        }
    }

    let total_findings = project.findings.len();
    let frontier_id = project
        .frontier_id
        .clone()
        .unwrap_or_else(|| String::from("<unknown>"));

    if json {
        let row_value = |row: &(String, Vec<String>)| {
            serde_json::json!({
                "finding_id": row.0,
                "discord_kinds": row.1,
            })
        };
        let report = serde_json::json!({
            "frontier_id": frontier_id,
            "total_findings": total_findings,
            "frontier_support_size": support.len(),
            "filtered_row_count": rows.len(),
            "filter_kind": kind_filter,
            "histogram": histogram,
            "rows": rows.iter().map(row_value).collect::<Vec<_>>(),
        });
        println!(
            "{}",
            serde_json::to_string_pretty(&report).expect("serialize discord report")
        );
        return;
    }

    println!("vela discord");
    println!("  frontier: {frontier_id}");
    println!("  total findings: {total_findings}");
    println!(
        "  frontier support (any discord): {} of {}",
        support.len(),
        total_findings
    );
    if let Some(k) = kind_filter {
        println!("  filter: kind = {k}");
    }
    println!();
    if histogram.is_empty() {
        println!("  no discord detected.");
    } else {
        println!("  discord histogram:");
        for (k, n) in &histogram {
            println!("    {n:>4}  {k}");
        }
    }
    if !rows.is_empty() {
        println!();
        println!("  findings with discord (showing up to 50):");
        for (fid, kinds) in rows.iter().take(50) {
            println!("    {fid}  ·  {}", kinds.join(", "));
        }
        if rows.len() > 50 {
            println!("    ... and {} more", rows.len() - 50);
        }
    }
}

fn empty_signal_report() -> signals::SignalReport {
    signals::SignalReport {
        schema: "vela.signals.v0".to_string(),
        frontier: "unavailable".to_string(),
        signals: Vec::new(),
        review_queue: Vec::new(),
        proof_readiness: signals::ProofReadiness {
            status: "unavailable".to_string(),
            blockers: 0,
            warnings: 0,
            caveats: vec!["Frontier could not be loaded for signal analysis.".to_string()],
        },
    }
}

fn print_signal_summary(report: &signals::SignalReport, strict: bool) {
    println!();
    println!("  {}", "SIGNALS".dimmed());
    println!("  {}", style::tick_row(60));
    println!("  total signals:   {}", report.signals.len());
    println!("  proof readiness: {}", report.proof_readiness.status);
    if !report.review_queue.is_empty() {
        println!("  review queue:    {} items", report.review_queue.len());
    }
    if strict && report.proof_readiness.status != "ready" {
        println!(
            "  {} proof readiness has blocking signals.",
            style::lost("strict check failed")
        );
    }
}

fn append_packet_json_file(
    packet_dir: &Path,
    relative_path: &str,
    value: &Value,
) -> Result<(), String> {
    let content = serde_json::to_vec_pretty(value)
        .map_err(|e| format!("Failed to serialize packet JSON file: {e}"))?;
    let path = packet_dir.join(relative_path);
    if let Some(parent) = path.parent() {
        std::fs::create_dir_all(parent)
            .map_err(|e| format!("Failed to create {}: {e}", parent.display()))?;
    }
    std::fs::write(&path, &content)
        .map_err(|e| format!("Failed to write {}: {e}", path.display()))?;
    let entry = json!({
        "path": relative_path,
        "sha256": hex::encode(Sha256::digest(&content)),
        "bytes": content.len(),
    });

    for manifest_name in ["manifest.json", "packet.lock.json"] {
        let manifest_path = packet_dir.join(manifest_name);
        let data = std::fs::read_to_string(&manifest_path)
            .map_err(|e| format!("Failed to read {}: {e}", manifest_path.display()))?;
        let mut manifest: Value = serde_json::from_str(&data)
            .map_err(|e| format!("Failed to parse {}: {e}", manifest_path.display()))?;
        let array_key = if manifest_name == "manifest.json" {
            "included_files"
        } else {
            "files"
        };
        let files = manifest
            .get_mut(array_key)
            .and_then(Value::as_array_mut)
            .ok_or_else(|| format!("{} missing {array_key} array", manifest_path.display()))?;
        files.retain(|file| {
            file.get("path")
                .and_then(Value::as_str)
                .is_none_or(|path| path != relative_path)
        });
        files.push(entry.clone());
        std::fs::write(
            &manifest_path,
            serde_json::to_vec_pretty(&manifest)
                .map_err(|e| format!("Failed to serialize {}: {e}", manifest_path.display()))?,
        )
        .map_err(|e| format!("Failed to write {}: {e}", manifest_path.display()))?;
    }

    let lock_path = packet_dir.join("packet.lock.json");
    let lock_content = std::fs::read(&lock_path)
        .map_err(|e| format!("Failed to read {}: {e}", lock_path.display()))?;
    let lock_entry = json!({
        "path": "packet.lock.json",
        "sha256": hex::encode(Sha256::digest(&lock_content)),
        "bytes": lock_content.len(),
    });
    let manifest_path = packet_dir.join("manifest.json");
    let data = std::fs::read_to_string(&manifest_path)
        .map_err(|e| format!("Failed to read {}: {e}", manifest_path.display()))?;
    let mut manifest: Value = serde_json::from_str(&data)
        .map_err(|e| format!("Failed to parse {}: {e}", manifest_path.display()))?;
    let files = manifest
        .get_mut("included_files")
        .and_then(Value::as_array_mut)
        .ok_or_else(|| format!("{} missing included_files array", manifest_path.display()))?;
    files.retain(|file| {
        file.get("path")
            .and_then(Value::as_str)
            .is_none_or(|path| path != "packet.lock.json")
    });
    files.push(lock_entry);
    std::fs::write(
        &manifest_path,
        serde_json::to_vec_pretty(&manifest)
            .map_err(|e| format!("Failed to serialize {}: {e}", manifest_path.display()))?,
    )
    .map_err(|e| format!("Failed to write {}: {e}", manifest_path.display()))?;
    Ok(())
}

fn print_tool_check_report(report: &Value) {
    let summary = report.get("summary").unwrap_or(&Value::Null);
    let frontier = report.get("frontier").unwrap_or(&Value::Null);
    println!();
    println!("  {}", "VELA · SERVE · CHECK-TOOLS".dimmed());
    println!("  {}", style::tick_row(60));
    println!(
        "frontier: {}",
        frontier
            .get("name")
            .and_then(Value::as_str)
            .unwrap_or("unknown")
    );
    println!(
        "findings: {}",
        frontier
            .get("findings")
            .and_then(Value::as_u64)
            .unwrap_or_default()
    );
    println!(
        "checks: {} passed, {} failed",
        summary
            .get("passed")
            .and_then(Value::as_u64)
            .unwrap_or_default(),
        summary
            .get("failed")
            .and_then(Value::as_u64)
            .unwrap_or_default()
    );
    if let Some(tools) = report.get("tools").and_then(Value::as_array) {
        let names = tools
            .iter()
            .filter_map(Value::as_str)
            .collect::<Vec<_>>()
            .join(", ");
        println!("tools: {names}");
    }
    if let Some(checks) = report.get("checks").and_then(Value::as_array) {
        for check in checks {
            let status = if check.get("ok").and_then(Value::as_bool) == Some(true) {
                style::ok("ok")
            } else {
                style::lost("lost")
            };
            println!(
                "  {} {}",
                status,
                check
                    .get("tool")
                    .and_then(Value::as_str)
                    .unwrap_or("unknown")
            );
        }
    }
}

fn print_state_report(report: &state::StateCommandReport, json_output: bool) {
    if json_output {
        println!(
            "{}",
            serde_json::to_string_pretty(report).expect("failed to serialize state command report")
        );
    } else {
        println!("{}", report.message);
        println!("  frontier: {}", report.frontier);
        println!("  finding:  {}", report.finding_id);
        println!("  proposal: {}", report.proposal_id);
        println!("  status:   {}", report.proposal_status);
        if let Some(event_id) = &report.applied_event_id {
            println!("  event:    {}", event_id);
        }
        println!("  wrote:    {}", report.wrote_to);
    }
}

fn print_history(payload: &Value) {
    let finding = payload.get("finding").unwrap_or(&Value::Null);
    println!("vela history");
    println!(
        "  finding: {}",
        finding
            .get("id")
            .and_then(Value::as_str)
            .unwrap_or("unknown")
    );
    println!(
        "  assertion: {}",
        finding
            .get("assertion")
            .and_then(Value::as_str)
            .unwrap_or("")
    );
    println!(
        "  confidence: {:.3}",
        finding
            .get("confidence")
            .and_then(Value::as_f64)
            .unwrap_or_default()
    );
    let reviews = payload
        .get("review_events")
        .and_then(Value::as_array)
        .map_or(0, Vec::len);
    let updates = payload
        .get("confidence_updates")
        .and_then(Value::as_array)
        .map_or(0, Vec::len);
    let annotations = finding
        .get("annotations")
        .and_then(Value::as_array)
        .map_or(0, Vec::len);
    let sources = payload
        .get("sources")
        .and_then(Value::as_array)
        .map_or(0, Vec::len);
    let atoms = payload
        .get("evidence_atoms")
        .and_then(Value::as_array)
        .map_or(0, Vec::len);
    let conditions = payload
        .get("condition_records")
        .and_then(Value::as_array)
        .map_or(0, Vec::len);
    let proposals = payload
        .get("proposals")
        .and_then(Value::as_array)
        .map_or(0, Vec::len);
    let events = payload
        .get("events")
        .and_then(Value::as_array)
        .map_or(0, Vec::len);
    println!("  review events:      {reviews}");
    println!("  confidence updates: {updates}");
    println!("  annotations:        {annotations}");
    println!("  sources:            {sources}");
    println!("  evidence atoms:     {atoms}");
    println!("  condition records:  {conditions}");
    println!("  proposals:          {proposals}");
    println!("  canonical events:   {events}");
    if let Some(status) = payload
        .get("proof_state")
        .and_then(|value| value.get("latest_packet"))
        .and_then(|value| value.get("status"))
        .and_then(Value::as_str)
    {
        println!("  proof state:        {status}");
    }
    if let Some(events) = payload.get("review_events").and_then(Value::as_array) {
        for event in events.iter().take(8) {
            println!(
                "  - {} {} {}",
                event
                    .get("reviewed_at")
                    .and_then(Value::as_str)
                    .unwrap_or(""),
                event.get("id").and_then(Value::as_str).unwrap_or(""),
                event.get("reason").and_then(Value::as_str).unwrap_or("")
            );
        }
    }
}

#[derive(Debug, Serialize)]
pub struct ProofTrace {
    pub trace_version: String,
    pub command: Vec<String>,
    pub source: String,
    pub source_hash: String,
    pub schema_version: String,
    pub checked_artifacts: Vec<String>,
    pub benchmark: Option<Value>,
    pub packet_manifest: String,
    pub packet_validation: String,
    pub caveats: Vec<String>,
    pub status: String,
    pub trace_path: String,
}

const SCIENCE_SUBCOMMANDS: &[&str] = &[
    "compile-notes",
    "compile-code",
    "compile-data",
    "review-pending",
    "find-tensions",
    "plan-experiments",
    "scout",
    "check",
    "normalize",
    "integrity",
    "impact",
    "discord",
    "quickstart",
    "proof",
    "repo",
    "serve",
    "stats",
    "search",
    "tensions",
    "gaps",
    "bridge",
    "export",
    "packet",
    "bench",
    "conformance",
    "version",
    "sign",
    "actor",
    "frontier",
    "queue",
    "registry",
    "init",
    "import",
    "lock",
    "doc",
    "diff",
    "proposals",
    "finding",
    "link",
    "entity",
    "review",
    "note",
    "caveat",
    "revise",
    "reject",
    "history",
    "import-events",
    "retract",
    "propagate",
    // v0.32: replication as a first-class kernel object.
    "replicate",
    "replications",
    // v0.33: computational provenance — datasets and code as
    // first-class kernel objects.
    "dataset-add",
    "datasets",
    "code-add",
    "code-artifacts",
    "artifact-add",
    "artifact-to-state",
    "bridge-kit",
    "source-adapter",
    "runtime-adapter",
    "artifacts",
    "artifact-audit",
    "decision-brief",
    "trial-summary",
    "source-verification",
    "source-ingest-plan",
    "clinical-trial-import",
    // v0.49: NegativeResult deposits (registered_trial + exploratory).
    "negative-result-add",
    "negative-results",
    // v0.50: Trajectory — search-path deposits.
    "trajectory-create",
    "trajectory-step",
    "trajectories",
    // v0.51: dual-use access tier classification.
    "tier-set",
    // v0.56: mechanical evidence-atom locator repair.
    "locator-repair",
    // v0.57: mechanical finding-level span repair.
    "span-repair",
    // v0.57: entity resolution.
    "entity-resolve",
    // v0.79: append a new entity tag to an existing finding.
    "entity-add",
    // v0.57: external source fetch (Crossref / PubMed / CT.gov).
    "source-fetch",
    // v0.34: predictions and resolutions — the epistemic accountability
    // ledger.
    "predict",
    "resolve",
    "predictions",
    "predictions-expire",
    "calibration",
    // v0.35: inference layer — consensus aggregation over claim-similar
    // findings.
    "consensus",
    // v0.39: federation — peer registry + sync runtime.
    "federation",
    // v0.40: causal reasoning — identifiability audit.
    "causal",
    // v0.42: daily-driver triad + conversational REPL. The
    // "git status / git log / inbox" of the substrate, plus a
    // thin natural-language router over the same kernel queries.
    "status",
    "log",
    "inbox",
    "ask",
    // v0.46: cross-frontier bridge runtime.
    "bridges",
    // v0.48: local workbench web app.
    "workbench",
    // v0.49: friendlier alias for `vela packet validate <path>`.
    "verify",
    // v0.74: top-level alias verbs that surface the daily flow
    // (init/ingest/propose/diff/accept/attest/log/lineage/serve)
    // without burying the verbs inside subcommand groups.
    "ingest",
    "propose",
    "accept",
    "attest",
    "lineage",
    // v0.75: Carina spec deliverable (list/schema/validate
    // against the 14 bundled primitive schemas).
    "carina",
    // v0.78: Atlas-level surface (init / materialize / serve).
    // Routes through handlers the binary installs.
    "atlas",
    // v0.82: Constellation-level surface (init / materialize /
    // serve). Network of Atlases (vco_*).
    "constellation",
];

pub fn is_science_subcommand(name: &str) -> bool {
    SCIENCE_SUBCOMMANDS.contains(&name)
}

fn print_strict_help() {
    println!(
        r#"Vela {}
Version control for scientific state.

Usage:
  vela <COMMAND>

Core flow (v0.74):
  init          Initialize a split frontier repo
  ingest        Ingest a paper, dataset, or Carina packet (dispatches by file type)
  propose       Create a finding.review proposal
  diff          Preview a `vpr_*` proposal, or compare two frontier files
  accept        Apply a proposal under reviewer authority
  attest        Sign findings under your private key
  log           Recent canonical state events
  lineage       State-transition replay for one finding
  serve         Local Workbench (findings, evidence, diff, lineage)

Read-only inspection:
  check         Validate a frontier, repo, or proof packet
  integrity     Check accepted frontier state integrity
  impact        Report downstream finding impact
  normalize     Apply deterministic frontier-state repairs
  proof         Export and validate a proof packet
  repo          Inspect split frontier repository status and shape
  stats         Show frontier statistics
  search        Search findings
  tensions      List candidate contradictions and tensions
  gaps          Inspect and rank candidate gap review leads
  bridge        Find candidate cross-domain connections

Advanced (proposal-creation, agent inboxes, federation):
  scout              Run Literature Scout against a folder of PDFs (writes proposals)
  compile-notes      Run Notes Compiler against a Markdown vault (writes proposals)
  compile-code       Run Code & Notebook Analyst against a research repo (writes proposals)
  compile-data       Run Datasets agent against a folder of CSV/TSV data (writes proposals)
  review-pending     Run Reviewer Agent: score every pending proposal (writes notes)
  find-tensions      Run Contradiction Finder: surface real contradictions among findings
  plan-experiments   Run Experiment Planner: propose experiments for open questions / hypotheses
  export        Export frontier artifacts
  packet        Inspect or validate proof packets
  bench         Run deterministic benchmark gates
  conformance   Run protocol conformance vectors
  sign          Optional signing and signature verification
  runtime-adapter
                Normalize external runtime exports into reviewable proposals
  version       Show version information
  import        Import frontier.json into a .vela repo
  proposals     Inspect, validate, export, import, accept, or reject write proposals
  artifact-to-state
                Import a Carina artifact packet as reviewable proposals
  bridge-kit
                Validate Carina artifact packets before importing runtime output
  source-adapter
                Run reviewed source adapters into artifact-to-state proposals
  finding       Add or manage finding bundles as frontier state
  link          Add typed links between findings (incl. cross-frontier vf_at-vfr targets)
  entity        Resolve unresolved entities against a bundled common-entity table (v0.19)
  frontier      Scaffold (`new`), materialize, and manage frontier metadata + deps
  actor         Register Ed25519 publisher identities in a frontier
  registry      Publish, list, or pull frontiers (open hub at https://vela-hub.fly.dev)
  review        Create a review proposal or review interactively
  note          Add a lightweight note to a finding
  caveat        Create an explicit caveat proposal
  revise        Create a confidence revision proposal
  reject        Create a rejection proposal
  history       Show state-transition history for one finding (v0.74 alias: `lineage`)
  import-events  Import review/state events from a packet or JSON file
  retract       Create a retraction proposal
  propagate     Simulate impact over declared dependency links
  artifact-add  Register a content-addressed artifact
  artifacts     List content-addressed artifacts
  artifact-audit Audit artifact locators, hashes, references, and profiles
  decision-brief Show the validated decision brief projection
  trial-summary Show the validated trial outcome projection
  source-verification Show the validated source verification projection
  source-ingest-plan Show the validated source ingest plan
  clinical-trial-import  Import a ClinicalTrials.gov record as an artifact
  locator-repair Mechanically repair an evidence atom's missing source locator
  span-repair    Mechanically repair a finding's missing evidence span
  entity-resolve Resolve a finding entity to a canonical id
  source-fetch   Fetch metadata + abstract for a doi:/pmid:/nct: source
  atlas         Compose multiple frontiers into a domain-level Atlas (vat_*) (v0.78+)
  constellation Compose multiple Atlases into a cross-domain Constellation (vco_*) (v0.82+)

Quick start (the demo):
  vela init demo --name "Your bounded question"
  vela ingest paper.pdf --frontier demo
  vela propose demo <vf_id> --status accepted --reason "..." --reviewer reviewer:you --apply
  vela diff <vpr_id> --frontier demo
  vela accept demo <vpr_id> --reviewer reviewer:you --reason "applied"
  vela serve --path demo

Substrate health:
  vela frontier materialize my-frontier --json
  vela repo status my-frontier --json
  vela proof verify my-frontier --json
  vela check my-frontier --strict --json

Monolithic frontier file:
  vela frontier new frontier.json --name "Your bounded question"
  vela finding add frontier.json --assertion "..." --author "reviewer:demo" --apply
  vela check frontier.json --json
  FINDING_ID=$(jq -r '.findings[0].id' frontier.json)
  vela review frontier.json "$FINDING_ID" --status contested --reason "Mouse-only evidence" --reviewer reviewer:demo --apply

Publish your own frontier (see docs/PUBLISHING.md):
  vela frontier new ./frontier.json --name "Your bounded question"
  vela finding add ./frontier.json --assertion "..." --author "reviewer:you" --apply
  vela sign generate-keypair --out keys
  vela actor add ./frontier.json reviewer:you --pubkey "$(cat keys/public.key)"
  vela registry publish ./frontier.json --owner reviewer:you --key keys/private.key \
      --to https://vela-hub.fly.dev
"#,
        env!("CARGO_PKG_VERSION")
    );
}

/// v0.22 Agent Inbox: pluggable handler for `vela scout`.
///
/// The substrate library can't import `vela-scientist` (cyclic
/// dependency), so the scout dispatch in this module looks up a
/// handler installed by the binary at startup. The `vela` CLI in
/// `crates/vela-cli` registers a real handler via
/// `register_scout_handler`. Library callers that want scout
/// behaviour install their own.
pub type ScoutHandler = fn(
    folder: PathBuf,
    frontier: PathBuf,
    backend: Option<String>,
    dry_run: bool,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static SCOUT_HANDLER: OnceLock<ScoutHandler> = OnceLock::new();

/// Install the scout handler. Idempotent — second registrations are
/// silently ignored so a misbehaving consumer can't unseat the
/// binary's wiring mid-run.
pub fn register_scout_handler(handler: ScoutHandler) {
    let _ = SCOUT_HANDLER.set(handler);
}

/// v0.78: pluggable handler for `vela atlas init`. The binary in
/// `vela-cli/src/main.rs` installs a real handler that calls into
/// the `vela-atlas` crate.
pub type AtlasInitHandler = fn(
    atlases_root: PathBuf,
    name: String,
    domain: String,
    scope_note: Option<String>,
    frontiers: Vec<PathBuf>,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static ATLAS_INIT_HANDLER: OnceLock<AtlasInitHandler> = OnceLock::new();

pub fn register_atlas_init_handler(handler: AtlasInitHandler) {
    let _ = ATLAS_INIT_HANDLER.set(handler);
}

/// v0.78: pluggable handler for `vela atlas materialize`.
pub type AtlasMaterializeHandler =
    fn(atlases_root: PathBuf, name: String, json: bool) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static ATLAS_MATERIALIZE_HANDLER: OnceLock<AtlasMaterializeHandler> = OnceLock::new();

pub fn register_atlas_materialize_handler(handler: AtlasMaterializeHandler) {
    let _ = ATLAS_MATERIALIZE_HANDLER.set(handler);
}

/// v0.78: pluggable handler for `vela atlas serve`. v0.78 stub
/// delegates to the per-frontier Workbench for the first
/// composing frontier. Dedicated Atlas-level Workbench page is
/// v0.79+.
pub type AtlasServeHandler = fn(
    atlases_root: PathBuf,
    name: String,
    port: u16,
    open_browser: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static ATLAS_SERVE_HANDLER: OnceLock<AtlasServeHandler> = OnceLock::new();

pub fn register_atlas_serve_handler(handler: AtlasServeHandler) {
    let _ = ATLAS_SERVE_HANDLER.set(handler);
}

/// v0.81.2: pluggable handler for `vela atlas update`. Lets the
/// binary update an Atlas's composing-frontier list without the
/// rm-and-init dance. The handler re-computes the Atlas's
/// content-addressed id and writes the updated manifest.
pub type AtlasUpdateHandler = fn(
    atlases_root: PathBuf,
    name: String,
    add_frontier: Vec<PathBuf>,
    remove_vfr_id: Vec<String>,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static ATLAS_UPDATE_HANDLER: OnceLock<AtlasUpdateHandler> = OnceLock::new();

pub fn register_atlas_update_handler(handler: AtlasUpdateHandler) {
    let _ = ATLAS_UPDATE_HANDLER.set(handler);
}

/// v0.82: Constellation-level handlers. Mirror the Atlas
/// pattern one layer up. The binary registers handlers that
/// call into the `vela-constellation` crate.
pub type ConstellationInitHandler = fn(
    constellations_root: PathBuf,
    name: String,
    scope_note: Option<String>,
    atlases: Vec<PathBuf>,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static CONSTELLATION_INIT_HANDLER: OnceLock<ConstellationInitHandler> = OnceLock::new();

pub fn register_constellation_init_handler(handler: ConstellationInitHandler) {
    let _ = CONSTELLATION_INIT_HANDLER.set(handler);
}

pub type ConstellationMaterializeHandler = fn(
    constellations_root: PathBuf,
    name: String,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static CONSTELLATION_MATERIALIZE_HANDLER: OnceLock<ConstellationMaterializeHandler> =
    OnceLock::new();

pub fn register_constellation_materialize_handler(handler: ConstellationMaterializeHandler) {
    let _ = CONSTELLATION_MATERIALIZE_HANDLER.set(handler);
}

pub type ConstellationServeHandler = fn(
    constellations_root: PathBuf,
    name: String,
    port: u16,
    open_browser: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static CONSTELLATION_SERVE_HANDLER: OnceLock<ConstellationServeHandler> = OnceLock::new();

pub fn register_constellation_serve_handler(handler: ConstellationServeHandler) {
    let _ = CONSTELLATION_SERVE_HANDLER.set(handler);
}

/// v0.23 Agent Inbox: pluggable handler for `vela compile-notes`.
/// Same OnceLock pattern as the scout handler; the binary
/// registers it at startup.
pub type NotesHandler = fn(
    vault: PathBuf,
    frontier: PathBuf,
    backend: Option<String>,
    max_files: Option<usize>,
    max_items_per_category: Option<usize>,
    dry_run: bool,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static NOTES_HANDLER: OnceLock<NotesHandler> = OnceLock::new();

/// Install the notes-compiler handler. Idempotent.
pub fn register_notes_handler(handler: NotesHandler) {
    let _ = NOTES_HANDLER.set(handler);
}

/// v0.24 Agent Inbox: pluggable handler for `vela compile-code`.
pub type CodeHandler = fn(
    root: PathBuf,
    frontier: PathBuf,
    backend: Option<String>,
    max_files: Option<usize>,
    dry_run: bool,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static CODE_HANDLER: OnceLock<CodeHandler> = OnceLock::new();

/// Install the code-analyst handler. Idempotent.
pub fn register_code_handler(handler: CodeHandler) {
    let _ = CODE_HANDLER.set(handler);
}

/// v0.25 Agent Inbox: pluggable handler for `vela compile-data`.
pub type DatasetsHandler = fn(
    root: PathBuf,
    frontier: PathBuf,
    backend: Option<String>,
    sample_rows: Option<usize>,
    dry_run: bool,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static DATASETS_HANDLER: OnceLock<DatasetsHandler> = OnceLock::new();

/// Install the datasets handler. Idempotent.
pub fn register_datasets_handler(handler: DatasetsHandler) {
    let _ = DATASETS_HANDLER.set(handler);
}

/// v0.28 Agent Inbox: handler for `vela review-pending`.
pub type ReviewerHandler = fn(
    frontier: PathBuf,
    backend: Option<String>,
    max_proposals: Option<usize>,
    batch_size: usize,
    dry_run: bool,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static REVIEWER_HANDLER: OnceLock<ReviewerHandler> = OnceLock::new();

/// Install the reviewer-agent handler. Idempotent.
pub fn register_reviewer_handler(handler: ReviewerHandler) {
    let _ = REVIEWER_HANDLER.set(handler);
}

/// v0.28 Agent Inbox: handler for `vela find-tensions`.
pub type TensionsHandler = fn(
    frontier: PathBuf,
    backend: Option<String>,
    max_findings: Option<usize>,
    dry_run: bool,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static TENSIONS_HANDLER: OnceLock<TensionsHandler> = OnceLock::new();

/// Install the contradiction-finder handler. Idempotent.
pub fn register_tensions_handler(handler: TensionsHandler) {
    let _ = TENSIONS_HANDLER.set(handler);
}

/// v0.28 Agent Inbox: handler for `vela plan-experiments`.
pub type ExperimentsHandler = fn(
    frontier: PathBuf,
    backend: Option<String>,
    max_findings: Option<usize>,
    dry_run: bool,
    json: bool,
) -> Pin<Box<dyn Future<Output = ()> + Send>>;

static EXPERIMENTS_HANDLER: OnceLock<ExperimentsHandler> = OnceLock::new();

/// Install the experiment-planner handler. Idempotent.
pub fn register_experiments_handler(handler: ExperimentsHandler) {
    let _ = EXPERIMENTS_HANDLER.set(handler);
}

// ── v0.47: session entry ─────────────────────────────────────────────
//
// Bare `vela` (no args) opens a session against the nearest `.vela/`
// repo, walking up from cwd. The session prints a one-screen
// dashboard, then accepts single-letter verb shortcuts or
// natural-language questions routed through `cmd_ask`.
//
// Doctrine: this is the daily-driver entry, not a kitchen-sink IDE.
// Single screen, no scroll, no full TUI redraw. Each verb spawns the
// existing kernel command and prints its output inline. The session
// stays out of the user's way: type something, get an answer, type
// again. OpenCode/Claude Code shape.

/// Walk up from `cwd` looking for a `.vela/` directory. Returns the
/// first parent that contains one, or `None` if none found.
fn find_vela_repo() -> Option<PathBuf> {
    let mut cur = std::env::current_dir().ok()?;
    loop {
        if cur.join(".vela").is_dir() {
            return Some(cur);
        }
        if !cur.pop() {
            return None;
        }
    }
}

fn print_session_help() {
    println!();
    println!(
        "  Vela {} · Version control for scientific state.",
        env!("CARGO_PKG_VERSION")
    );
    println!();
    println!("  USAGE");
    println!("    vela              Open a session against the nearest .vela/ repo");
    println!("    vela <command>    Run a specific subcommand");
    println!("    vela help advanced   Full subcommand list (30+ commands)");
    println!();
    println!("  CORE FLOW (v0.74)");
    println!("    init              Initialize a split frontier repo");
    println!("    ingest <path>     Ingest a paper, dataset, or Carina packet");
    println!("    propose           Create a finding.review proposal");
    println!("    diff <vpr_id>     Preview a pending proposal vs current frontier");
    println!("    accept <vpr_id>   Apply a proposal under reviewer authority");
    println!("    attest            Sign findings under your private key");
    println!("    log               Recent canonical state events");
    println!("    lineage <vf_id>   State-transition replay for one finding");
    println!("    serve             Local Workbench (find, evidence, diff, lineage)");
    println!();
    println!("  DAILY ALSO-RANS");
    println!("    status            One-screen frontier health");
    println!("    inbox             Pending review proposals");
    println!("    review            Review a proposal interactively");
    println!("    ask <question>    Plain-text query against the frontier");
    println!();
    println!("  REASONING (Pearl 1 → 2 → 3)");
    println!("    causal audit                       Per-finding identifiability");
    println!("    causal effect <src> --on <tgt>     Pairwise back-door / front-door");
    println!("    causal counterfactual <src> --target <tgt> --set-to <0..1>");
    println!();
    println!("  COMPOSITION");
    println!("    bridge <a> <b>                     Cross-frontier hypotheses");
    println!("    consensus <vf>                     Field consensus over similar claims");
    println!();
    println!("  PUBLISH");
    println!("    registry publish                   Push a signed manifest to the hub");
    println!("    federation peer-add                Federate with another hub");
    println!();
    println!("  In session, type a single letter for a quick verb, or any");
    println!("  question in plain text. `q` or `exit` quits.");
    println!();
}

fn print_session_dashboard(project: &crate::project::Project, repo_path: &Path) {
    use crate::causal_reasoning::{audit_frontier, summarize_audit};

    let label = frontier_label(project);
    let vfr = project.frontier_id();
    let vfr_short = vfr.chars().take(16).collect::<String>();

    let mut pending = 0usize;
    let mut by_kind: std::collections::BTreeMap<String, usize> = std::collections::BTreeMap::new();
    for p in &project.proposals {
        if p.status == "pending_review" {
            pending += 1;
            *by_kind.entry(p.kind.clone()).or_insert(0) += 1;
        }
    }

    let audit = audit_frontier(project);
    let audit_summary = summarize_audit(&audit);

    let bridges_dir = repo_path.join(".vela/bridges");
    let mut bridge_total = 0usize;
    let mut bridge_confirmed = 0usize;
    let mut bridge_derived = 0usize;
    if bridges_dir.is_dir()
        && let Ok(entries) = std::fs::read_dir(&bridges_dir)
    {
        for entry in entries.flatten() {
            let path = entry.path();
            if path.extension().and_then(|s| s.to_str()) != Some("json") {
                continue;
            }
            bridge_total += 1;
            if let Ok(data) = std::fs::read_to_string(&path)
                && let Ok(b) = serde_json::from_str::<crate::bridge::Bridge>(&data)
            {
                match b.status {
                    crate::bridge::BridgeStatus::Confirmed => bridge_confirmed += 1,
                    crate::bridge::BridgeStatus::Derived => bridge_derived += 1,
                    _ => {}
                }
            }
        }
    }

    let mut targets_with_success = std::collections::HashSet::new();
    let mut failed_replications = 0usize;
    for r in &project.replications {
        if r.outcome == "replicated" {
            targets_with_success.insert(r.target_finding.clone());
        } else if r.outcome == "failed" {
            failed_replications += 1;
        }
    }

    println!();
    let version = crate::project::VELA_COMPILER_VERSION
        .strip_prefix("vela/")
        .unwrap_or(crate::project::VELA_COMPILER_VERSION);
    println!(
        "  {}",
        format!("VELA · {version} · {label}")
            .to_uppercase()
            .dimmed()
    );
    println!("  {}", style::tick_row(60));
    println!(
        "  vfr_id     {}…   repo  {}",
        vfr_short,
        repo_path.display()
    );
    println!(
        "  findings   {:>4}     events   {}     proposals pending  {}",
        project.findings.len(),
        project.events.len(),
        pending
    );

    if pending > 0 {
        let parts: Vec<String> = by_kind.iter().map(|(k, n)| format!("{n} {k}")).collect();
        println!("  {}     · {}", style::warn("inbox"), parts.join("  "));
    }
    if audit_summary.underidentified > 0 || audit_summary.conditional > 0 {
        println!(
            "  {}     · {} underidentified · {} conditional",
            if audit_summary.underidentified > 0 {
                style::lost("audit")
            } else {
                style::warn("audit")
            },
            audit_summary.underidentified,
            audit_summary.conditional,
        );
    }
    if bridge_total > 0 {
        println!(
            "  {}   · {} total · {} confirmed · {} awaiting review",
            style::ok("bridges"),
            bridge_total,
            bridge_confirmed,
            bridge_derived
        );
    }
    if !project.replications.is_empty() {
        println!(
            "  {} · {} records · {} findings replicated · {} failed",
            style::ok("replications"),
            project.replications.len(),
            targets_with_success.len(),
            failed_replications,
        );
    }

    println!();
    println!("  type a verb or ask anything:");
    println!("    a  audit problems     i  inbox (pending)     b  bridges");
    println!("    g  causal graph       l  log (recent)        c  counterfactuals");
    println!("    s  refresh status     h  help (more verbs)   q  quit");
    println!();
}

/// Run a single verb shortcut. Returns true if the verb was recognized.
fn run_session_verb(verb: &str, repo_path: &Path) -> bool {
    match verb {
        "a" | "audit" => {
            let action = CausalAction::Audit {
                frontier: repo_path.to_path_buf(),
                problems_only: true,
                json: false,
            };
            cmd_causal(action);
            true
        }
        "i" | "inbox" => {
            let action = ProposalAction::List {
                frontier: repo_path.to_path_buf(),
                status: Some("pending_review".into()),
                json: false,
            };
            cmd_proposals(action);
            true
        }
        "b" | "bridges" => {
            let action = BridgesAction::List {
                frontier: repo_path.to_path_buf(),
                status: None,
                json: false,
            };
            cmd_bridges(action);
            true
        }
        "g" | "graph" => {
            let action = CausalAction::Graph {
                frontier: repo_path.to_path_buf(),
                node: None,
                json: false,
            };
            cmd_causal(action);
            true
        }
        "l" | "log" => {
            cmd_log(repo_path, 10, None, false);
            true
        }
        "c" | "counterfactual" | "counterfactuals" => {
            // No specific source/target — print the live pairs the
            // user can run counterfactual queries against.
            let project = match repo::load_from_path(repo_path) {
                Ok(p) => p,
                Err(e) => {
                    eprintln!("{} {e}", style::err_prefix());
                    return true;
                }
            };
            println!();
            println!("  {}", "VELA · COUNTERFACTUAL · LIVE PAIRS".dimmed());
            println!("  {}", style::tick_row(60));
            // Walk every finding's `depends`/`supports` links; a live
            // counterfactual pair is (target, child) where the link
            // from child to target carries a mechanism.
            let mut pairs = 0usize;
            for child in &project.findings {
                for link in &child.links {
                    if !matches!(link.link_type.as_str(), "depends" | "supports") {
                        continue;
                    }
                    if link.mechanism.is_none() {
                        continue;
                    }
                    let parent = link
                        .target
                        .split_once(':')
                        .map_or(link.target.as_str(), |(_, r)| r);
                    pairs += 1;
                    if pairs <= 10 {
                        println!("    · do({parent}) → {}", child.id);
                    }
                }
            }
            if pairs == 0 {
                println!("  no mechanism-annotated edges found.");
                println!("  add a mechanism via the link's `mechanism` field; see /counterfactual");
            } else {
                println!();
                println!("  {pairs} live pair(s). Run with:");
                println!("    vela causal counterfactual <repo> <src> --target <tgt> --set-to 0.5");
            }
            println!();
            true
        }
        "s" | "status" | "refresh" => {
            // Reload + re-render dashboard.
            match repo::load_from_path(repo_path) {
                Ok(p) => print_session_dashboard(&p, repo_path),
                Err(e) => eprintln!("{} {e}", style::err_prefix()),
            }
            true
        }
        "h" | "help" | "?" => {
            print_session_help();
            true
        }
        _ => false,
    }
}

fn run_session() {
    let repo_path = match find_vela_repo() {
        Some(p) => p,
        None => {
            println!();
            println!(
                "  {}",
                "VELA · NO FRONTIER FOUND IN CWD OR ANY PARENT".dimmed()
            );
            println!("  {}", style::tick_row(60));
            println!("  Run `vela init` here to create a frontier, or cd into one.");
            println!("  Or run `vela help` for the command list.");
            println!();
            return;
        }
    };

    let project = match repo::load_from_path(&repo_path) {
        Ok(p) => p,
        Err(e) => {
            eprintln!("{} failed to load .vela/ repo: {e}", style::err_prefix());
            std::process::exit(1);
        }
    };

    print_session_dashboard(&project, &repo_path);

    use std::io::{BufRead, Write};
    let stdin = std::io::stdin();
    let mut stdout = std::io::stdout();
    loop {
        print!("  > ");
        stdout.flush().ok();
        let mut line = String::new();
        if stdin.lock().read_line(&mut line).is_err() {
            break;
        }
        let input = line.trim();
        if input.is_empty() {
            continue;
        }
        if matches!(input, "q" | "quit" | "exit") {
            break;
        }
        if run_session_verb(input, &repo_path) {
            continue;
        }
        // Fall through: treat as natural-language question.
        let project = match repo::load_from_path(&repo_path) {
            Ok(p) => p,
            Err(e) => {
                eprintln!("{} {e}", style::err_prefix());
                continue;
            }
        };
        answer(&project, input, false);
    }
}

pub fn run_from_args() {
    style::init();
    let args = std::env::args().collect::<Vec<_>>();
    match args.get(1).map(String::as_str) {
        // v0.47: bare `vela` opens a session against the nearest
        // `.vela/` repo. The 30+ subcommand list is still there for
        // direct invocation; the session is the daily-driver entry.
        None => {
            run_session();
            return;
        }
        Some("-h" | "--help" | "help") => {
            // v0.47: top-level help shows the daily flow. The full
            // 30+ subcommand list lives behind `vela help advanced`.
            if args.get(2).map(String::as_str) == Some("advanced") {
                print_strict_help();
            } else {
                print_session_help();
            }
            return;
        }
        Some("-V" | "--version" | "version") => {
            println!("vela {}", env!("CARGO_PKG_VERSION"));
            return;
        }
        Some("proof") if args.get(2).map(String::as_str) == Some("verify") => {
            let json = args.iter().any(|arg| arg == "--json");
            let frontier = args
                .iter()
                .skip(3)
                .find(|arg| !arg.starts_with('-'))
                .map(PathBuf::from)
                .unwrap_or_else(|| {
                    eprintln!(
                        "{} proof verify requires a frontier repo",
                        style::err_prefix()
                    );
                    std::process::exit(2);
                });
            cmd_proof_verify(&frontier, json);
            return;
        }
        Some("proof") if args.get(2).map(String::as_str) == Some("explain") => {
            let frontier = args
                .iter()
                .skip(3)
                .find(|arg| !arg.starts_with('-'))
                .map(PathBuf::from)
                .unwrap_or_else(|| {
                    eprintln!(
                        "{} proof explain requires a frontier repo",
                        style::err_prefix()
                    );
                    std::process::exit(2);
                });
            cmd_proof_explain(&frontier);
            return;
        }
        Some(cmd) if !is_science_subcommand(cmd) => {
            eprintln!(
                "{} unknown or non-release command: {cmd}",
                style::err_prefix()
            );
            eprintln!("run `vela --help` for the strict v0 command surface.");
            std::process::exit(2);
        }
        Some(_) => {}
    }
    let runtime = tokio::runtime::Runtime::new().expect("failed to create tokio runtime");
    runtime.block_on(run_command());
}

fn fail(message: &str) -> ! {
    eprintln!("{} {message}", style::err_prefix());
    std::process::exit(1);
}

/// Validate that a CLI string argument is one of the allowed enum values.
/// On mismatch, prints a friendly error naming the flag and the valid set
/// and exits with code 1. Used at finding-add time so users learn before
/// strict validation rejects the resulting frontier.
fn validate_enum_arg(flag: &str, value: &str, valid: &[&str]) {
    if !valid.contains(&value) {
        fail(&format!(
            "invalid {flag} '{value}'. Valid: {}",
            valid.join(", ")
        ));
    }
}

fn fail_return<T>(message: &str) -> T {
    fail(message)
}