open-kioku-cli 1.0.4

use clap::{Args, Parser, Subcommand, ValueEnum};
use open_kioku_architecture::ArchitectureDetector;
use open_kioku_config::{OkConfig, ScipMode};
use open_kioku_context::{ContextPackBuilder, ContextPackFormat};
use open_kioku_context_compress::ContextHandleStore;
use open_kioku_core::{Confidence, ContextHandleId, IndexManifest};
use open_kioku_graph::InMemoryGraph;
use open_kioku_impact::ImpactEngine;
use open_kioku_ingest::{IndexProgress, Indexer};
use open_kioku_memory::RepoMemoryStore;
use open_kioku_patch::PatchPlanner;
use open_kioku_plan::{PlanEngine, PlanFormat};
use open_kioku_search_regex::search_chunks;
use open_kioku_search_tantivy::{default_index_dir, rebuild_disk_index, TantivySearchIndex};
use open_kioku_storage::{GraphStore, IndexData, MetadataStore, OkStore, SearchIndex};
use open_kioku_storage_sqlite::SqliteStore;
use open_kioku_symbols::SymbolEngine;
use open_kioku_tests::TestSelector;
use serde::Serialize;
use std::collections::BTreeMap;
use std::fs;
use std::path::{Path, PathBuf};
use std::sync::{Arc, Mutex};
use std::thread;
use std::time::{Duration, Instant};

#[derive(Parser)]
#[command(name = "ok", version, about = "Open Kioku code-intelligence platform")]
struct Cli {
    #[arg(long, global = true)]
    json: bool,
    #[arg(long, global = true, default_value = ".")]
    repo: PathBuf,
    #[command(subcommand)]
    command: Command,
}

#[derive(Subcommand)]
enum Command {
    Init {
        #[arg(default_value = ".")]
        repo: PathBuf,
    },
    Index {
        #[arg(default_value = ".")]
        repo: PathBuf,
        #[arg(long = "with-scip", value_parser = ["off", "consume", "auto", "required"])]
        with_scip: Option<String>,
    },
    /// Keep the local index current while repository files change.
    Watch {
        #[arg(default_value = ".")]
        repo: PathBuf,
    },
    Status {
        #[arg(default_value = ".")]
        repo: PathBuf,
        /// Render a portable Markdown status snapshot.
        #[arg(long, default_value_t = false)]
        markdown: bool,
        /// Write the Markdown status snapshot to a file.
        #[arg(long, value_name = "PATH")]
        write: Option<PathBuf>,
        /// Exit non-zero when readiness checks fail.
        #[arg(long, default_value_t = false)]
        exit_code: bool,
    },
    Doctor {
        #[arg(default_value = ".")]
        repo: PathBuf,
    },
    Setup {
        #[command(subcommand)]
        command: SetupCommand,
    },
    Demo {
        #[arg(long)]
        path: Option<PathBuf>,
        #[arg(long, default_value_t = false)]
        force: bool,
    },
    Search {
        query: String,
        #[arg(long, default_value_t = 20)]
        limit: usize,
    },
    Symbol {
        #[command(subcommand)]
        command: SymbolCommand,
    },
    Explain {
        #[command(subcommand)]
        command: ExplainCommand,
    },
    Impact(ImpactArgs),
    Path {
        from: String,
        to: String,
    },
    Tests {
        #[arg(long)]
        changed: PathBuf,
    },
    Context {
        task: String,
        #[arg(long, value_enum, default_value_t = ContextPackFormat::Json)]
        format: ContextPackFormat,
        #[arg(long, default_value_t = false)]
        compressed: bool,
    },
    RetrieveContext {
        handle: String,
    },
    Plan {
        task: String,
        #[arg(long, value_enum, default_value_t = PlanFormat::Text)]
        format: PlanFormat,
        #[arg(long, default_value_t = 12)]
        limit: usize,
    },
    Bench(BenchArgs),
    Eval(EvalArgs),
    Prove(ProveArgs),

    Architecture {
        #[command(subcommand)]
        command: ArchitectureCommand,
    },
    Patch {
        #[command(subcommand)]
        command: PatchCommand,
    },
    Memory {
        #[command(subcommand)]
        command: MemoryCommand,
    },
    Mcp {
        #[command(subcommand)]
        command: McpCommand,
    },
    Scip {
        #[command(subcommand)]
        command: ScipCommand,
    },
}

#[derive(Debug, Clone, Copy, PartialEq, Eq, ValueEnum)]
enum ConfidenceArg {
    Low,
    Medium,
    High,
    Exact,
}

impl From<ConfidenceArg> for Confidence {
    fn from(value: ConfidenceArg) -> Self {
        match value {
            ConfidenceArg::Low => Self::Low,
            ConfidenceArg::Medium => Self::Medium,
            ConfidenceArg::High => Self::High,
            ConfidenceArg::Exact => Self::Exact,
        }
    }
}

#[derive(Subcommand)]
enum MemoryCommand {
    Remember {
        text: String,
        #[arg(long, default_value = "cli")]
        source: String,
        #[arg(long, value_enum, default_value_t = ConfidenceArg::Medium)]
        confidence: ConfidenceArg,
    },
    Search {
        query: String,
        #[arg(long, default_value_t = 10)]
        limit: usize,
    },
    Recent {
        #[arg(long, default_value_t = 20)]
        limit: usize,
    },
}

#[derive(Subcommand)]
enum SetupCommand {
    /// Audit install readiness across index, security, MCP, and client surfaces.
    Audit {
        #[arg(default_value = ".")]
        repo: PathBuf,
        /// Render a portable Markdown setup report.
        #[arg(long, default_value_t = false)]
        markdown: bool,
        /// Write the Markdown setup report to a file.
        #[arg(long, value_name = "PATH")]
        write: Option<PathBuf>,
        /// Exit non-zero when required setup checks fail.
        #[arg(long, default_value_t = false)]
        exit_code: bool,
    },
}

#[derive(Args)]
struct BenchArgs {
    /// Repository to index and benchmark.
    #[arg(default_value = ".")]
    path: PathBuf,

    /// Search quality expectation as QUERY=EXPECTED_PATH_SUBSTRING.
    #[arg(long = "quality-case", value_name = "QUERY=EXPECTED_PATH")]
    quality_cases: Vec<String>,

    /// Number of search results considered for each quality case.
    #[arg(long, default_value_t = 10)]
    quality_limit: usize,

    /// Fail when quality precision@1 is below this threshold.
    #[arg(long, default_value_t = 0.0)]
    quality_min_precision_at_1: f64,
}

#[derive(Args)]
struct ProveArgs {
    /// Repository to index and evaluate.
    #[arg(default_value = ".")]
    path: PathBuf,

    /// Task to evaluate. Repeat to score multiple workflows.
    #[arg(long = "task", value_name = "TASK")]
    tasks: Vec<String>,

    /// Output format for the shareable proof report.
    #[arg(long, value_enum, default_value_t = ProveFormat::Markdown)]
    format: ProveFormat,

    /// Maximum context results considered by each plan.
    #[arg(long, default_value_t = 12)]
    limit: usize,

    /// Include repository-relative paths instead of redacted path shapes.
    #[arg(long, default_value_t = false)]
    reveal_paths: bool,
}

#[derive(Args)]
struct EvalArgs {
    /// Repository to index and evaluate.
    #[arg(default_value = ".")]
    path: PathBuf,

    /// Golden case as TASK=EXPECTED_PATH[,EXPECTED_PATH...].
    #[arg(long = "case", value_name = "TASK=EXPECTED_PATHS")]
    cases: Vec<String>,

    /// JSON file containing [{ "task": "...", "expected_paths": [...], "expected_tests": [...] }].
    #[arg(long)]
    cases_file: Option<PathBuf>,

    /// Number of search/context/test results considered for each case.
    #[arg(long, default_value_t = 10)]
    limit: usize,

    /// Fail when search recall@k is below this threshold.
    #[arg(long, default_value_t = 0.0)]
    min_recall_at_k: f64,

    /// Fail when mean reciprocal rank is below this threshold.
    #[arg(long, default_value_t = 0.0)]
    min_mrr: f64,
}

#[derive(Debug, Clone, Copy, PartialEq, Eq, ValueEnum)]
enum ProveFormat {
    Markdown,
    Json,
}

#[derive(Subcommand)]
enum SymbolCommand {
    Find { name: String },
    Definition { name: String },
    Refs { name: String },
}

#[derive(Subcommand)]
enum ExplainCommand {
    File { path: PathBuf },
    Symbol { name: String },
}

#[derive(Args)]
struct ImpactArgs {
    #[arg(long)]
    file: Option<PathBuf>,
    #[arg(long)]
    symbol: Option<String>,
}

#[derive(Subcommand)]
enum ArchitectureCommand {
    Detect,
    Boundaries,
    Violations,
}

#[derive(Subcommand)]
enum PatchCommand {
    Plan {
        task: String,
    },
    Review {
        #[arg(long)]
        id: String,
    },
    Apply {
        #[arg(long)]
        id: String,
        #[arg(long)]
        approved: bool,
    },
}

#[derive(Subcommand)]
enum McpCommand {
    Install {
        client: McpClient,
        #[arg(long, default_value = ".")]
        repo: PathBuf,
    },
    Serve {
        #[arg(long, default_value = ".")]
        repo: PathBuf,
        #[arg(long, default_value_t = true)]
        read_only: bool,
        #[arg(long, default_value_t = false)]
        allow_write: bool,
        #[arg(long, default_value_t = true)]
        approval_required: bool,
        #[arg(long = "allow-command")]
        allow_command: Vec<String>,
        #[arg(long, default_value_t = true)]
        deny_network: bool,
        #[arg(long, default_value_t = false)]
        hide_experimental: bool,
    },
}

#[derive(Subcommand)]
enum ScipCommand {
    Doctor {
        #[arg(default_value = ".")]
        repo: PathBuf,
    },
    Setup {
        #[arg(default_value = ".")]
        repo: PathBuf,
    },
}

#[derive(Clone, Copy, ValueEnum)]
enum McpClient {
    Claude,
    Cursor,
    Codex,
    Gemini,
    Opencode,
    Zed,
}

impl McpClient {
    fn as_str(self) -> &'static str {
        match self {
            Self::Claude => "claude",
            Self::Cursor => "cursor",
            Self::Codex => "codex",
            Self::Gemini => "gemini",
            Self::Opencode => "opencode",
            Self::Zed => "zed",
        }
    }

    fn config_format(self) -> &'static str {
        match self {
            Self::Codex => "toml",
            _ => "json",
        }
    }
}

#[derive(Debug, Clone)]
struct QualityCase {
    query: String,
    expected_path: String,
}

#[derive(Serialize)]
struct BenchReport {
    repo: PathBuf,
    index: IndexBenchReport,
    search: SearchBenchReport,
    quality: Option<QualityBenchReport>,
}

#[derive(Serialize)]
struct IndexBenchReport {
    file_count: usize,
    symbol_count: usize,
    chunk_count: usize,
    elapsed_ms: f64,
    files_per_second: f64,
}

#[derive(Serialize)]
struct SearchBenchReport {
    bm25_median_ms: f64,
    regex_median_ms: f64,
}

#[derive(Serialize)]
struct QualityBenchReport {
    case_count: usize,
    precision_at_1: f64,
    hit_rate_at_k: f64,
    mean_reciprocal_rank: f64,
    limit: usize,
    cases: Vec<QualityCaseReport>,
}

#[derive(Serialize)]
struct QualityCaseReport {
    query: String,
    expected_path: String,
    rank: Option<usize>,
    top_path: Option<PathBuf>,
    matched_path: Option<PathBuf>,
    result_count: usize,
}

#[derive(Serialize)]
struct ProofReport {
    repo: String,
    generated_by: &'static str,
    privacy: ProofPrivacy,
    summary: ProofSummary,
    languages: BTreeMap<String, usize>,
    tasks: Vec<ProofTaskReport>,
    reproduce: Vec<String>,
    notes: Vec<&'static str>,
}

#[derive(Serialize)]
struct ProofPrivacy {
    source_snippets_included: bool,
    local_root_included: bool,
    path_mode: &'static str,
}

#[derive(Serialize)]
struct ProofSummary {
    indexed_files: usize,
    indexed_symbols: usize,
    indexed_chunks: usize,
    tasks_scored: usize,
    average_score: f64,
    min_score: u32,
    max_score: u32,
    pass_rate_70: f64,
}

#[derive(Serialize)]
struct ProofTaskReport {
    task: String,
    score: u32,
    checks: BTreeMap<&'static str, bool>,
    primary_context_count: usize,
    source_context_count: usize,
    impact_count: usize,
    validation_count: usize,
    tool_call_count: usize,
    risk_level: String,
    sample_paths: Vec<String>,
    top_search_paths: Vec<String>,
}

#[derive(Debug, Clone, Serialize, serde::Deserialize)]
struct EvalCase {
    task: String,
    #[serde(default)]
    expected_paths: Vec<String>,
    #[serde(default)]
    expected_tests: Vec<String>,
}

#[derive(Serialize)]
struct EvalReport {
    repo: PathBuf,
    limit: usize,
    case_count: usize,
    summary: EvalSummary,
    cases: Vec<EvalCaseReport>,
}

#[derive(Serialize)]
struct EvalSummary {
    search_recall_at_k: f64,
    search_mrr: f64,
    search_ndcg_at_k: f64,
    context_recall_at_k: f64,
    test_recall_at_k: f64,
    abstention_required: usize,
}

#[derive(Serialize)]
struct EvalCaseReport {
    task: String,
    expected_paths: Vec<String>,
    expected_tests: Vec<String>,
    search_ranks: Vec<Option<usize>>,
    context_hits: Vec<String>,
    test_hits: Vec<String>,
    top_search_paths: Vec<PathBuf>,
    top_context_paths: Vec<PathBuf>,
    confidence: &'static str,
    notes: Vec<String>,
}

#[derive(Serialize)]
struct DoctorReport {
    ok: bool,
    repo: PathBuf,
    checks: Vec<DoctorCheck>,
    next_steps: Vec<String>,
}

#[derive(Serialize)]
struct SetupAuditReport {
    ok: bool,
    repo: PathBuf,
    generated_by: &'static str,
    checks: Vec<SetupAuditCheck>,
    providers: Vec<QualityProviderReport>,
    advanced_providers: Vec<QualityProviderReport>,
    clients: Vec<ClientInstallReport>,
    plugin_surfaces: Vec<PluginSurfaceReport>,
    next_steps: Vec<String>,
}

#[derive(Serialize)]
struct SetupAuditCheck {
    name: String,
    status: CheckStatus,
    message: String,
}

#[derive(Serialize)]
struct ClientInstallReport {
    client: &'static str,
    config_format: &'static str,
    install_command: String,
    verify: String,
    note: &'static str,
}

#[derive(Serialize)]
struct PluginSurfaceReport {
    name: &'static str,
    path: PathBuf,
    present: bool,
    note: &'static str,
}

#[derive(Serialize)]
struct QualityProviderReport {
    name: &'static str,
    status: CheckStatus,
    evidence: String,
    next_step: Option<String>,
}

#[derive(Serialize)]
struct DemoReport {
    repo: PathBuf,
    file_count: usize,
    symbol_count: usize,
    chunk_count: usize,
    commands: Vec<String>,
}

#[derive(Serialize)]
struct DoctorCheck {
    name: &'static str,
    status: CheckStatus,
    message: String,
}

#[derive(Serialize)]
struct ScipSetupReport {
    repo: PathBuf,
    mode: String,
    enabled: bool,
    allow_install: bool,
    timeout_seconds: u64,
    indexers: Vec<ScipIndexerReport>,
    configured_paths: Vec<PathBuf>,
}

#[derive(Serialize)]
struct ScipIndexerReport {
    language: &'static str,
    applicable: bool,
    installed: bool,
    command: String,
    output_path: PathBuf,
    note: String,
}

#[derive(Debug, Clone, Copy, Serialize)]
#[serde(rename_all = "snake_case")]
enum CheckStatus {
    Pass,
    Warn,
    Fail,
}

impl CheckStatus {
    fn label(self) -> &'static str {
        match self {
            Self::Pass => "pass",
            Self::Warn => "warn",
            Self::Fail => "fail",
        }
    }

    fn marker(self) -> &'static str {
        match self {
            Self::Pass => "[ok]",
            Self::Warn => "[warn]",
            Self::Fail => "[fail]",
        }
    }
}

#[tokio::main]
async fn main() -> anyhow::Result<()> {
    tracing_subscriber::fmt().with_env_filter("warn").init();
    let cli = Cli::parse();
    let repo = cli.repo.clone();
    match cli.command {
        Command::Init { repo: command_repo } => {
            let repo = resolve_repo(&repo, command_repo);
            std::fs::create_dir_all(repo.join(".ok"))?;
            OkConfig::write_default(repo.join("ok.toml"))?;
            print_text_or_json(
                cli.json,
                "initialized Open Kioku repository",
                &serde_json::json!({"status":"initialized"}),
            )?;
        }
        Command::Index {
            repo: command_repo,
            with_scip,
        } => {
            let repo = resolve_repo(&repo, command_repo);
            let snapshot = index_repo_with_scip_mode(&repo, with_scip.as_deref())?;
            if cli.json {
                println!("{}", serde_json::to_string_pretty(&snapshot.manifest)?);
            } else {
                println!(
                    "Indexed {} files, {} symbols, {} chunks",
                    snapshot.manifest.file_count,
                    snapshot.manifest.symbol_count,
                    snapshot.manifest.chunk_count
                );
                if let Some(scip) = &snapshot.scip {
                    println!(
                        "SCIP: mode {:?}, imported {} index(es), {} exact references",
                        scip.mode,
                        scip.imported_paths.len(),
                        scip.exact_references
                    );
                    for attempt in &scip.generator_attempts {
                        println!(
                            "SCIP {}: {:?} - {}",
                            attempt.language, attempt.status, attempt.message
                        );
                    }
                }
            }
        }
        Command::Watch { repo: command_repo } => {
            let repo = resolve_repo(&repo, command_repo);
            open_kioku_watch::watch_repo(&repo)?;
        }
        Command::Status {
            repo: command_repo,
            markdown,
            write,
            exit_code,
        } => {
            let repo = resolve_repo(&repo, command_repo);
            let manifest = load_index_manifest(&repo)?;
            let doctor = if markdown || write.is_some() || exit_code {
                Some(doctor_report(&repo))
            } else {
                None
            };
            if markdown || write.is_some() {
                let doctor_ref = doctor
                    .as_ref()
                    .expect("doctor report should be available for status snapshot");
                let rendered = render_status_markdown(&repo, manifest.as_ref(), doctor_ref);
                if let Some(path) = write {
                    fs::write(&path, rendered)?;
                    if cli.json {
                        println!(
                            "{}",
                            serde_json::to_string_pretty(&serde_json::json!({
                                "ok": doctor_ref.ok,
                                "path": path,
                            }))?
                        );
                    } else {
                        println!("Wrote Open Kioku status snapshot to {}", path.display());
                    }
                } else {
                    println!("{rendered}");
                }
            } else if cli.json {
                println!("{}", serde_json::to_string_pretty(&manifest)?);
            } else if let Some(manifest) = manifest {
                println!(
                    "Healthy index: {} files, {} symbols, indexed at {}",
                    manifest.file_count, manifest.symbol_count, manifest.indexed_at
                );
            } else {
                println!("No index found. Run `ok index .`.");
            }
            if exit_code && !doctor.as_ref().map(|report| report.ok).unwrap_or(true) {
                anyhow::bail!("Open Kioku status has failing readiness checks");
            }
        }
        Command::Doctor { repo: command_repo } => {
            let repo = resolve_repo(&repo, command_repo);
            let report = doctor_report(&repo);
            let ok = report.ok;
            if cli.json {
                println!("{}", serde_json::to_string_pretty(&report)?);
            } else {
                println!("Open Kioku doctor for {}", report.repo.display());
                for check in &report.checks {
                    let marker = match check.status {
                        CheckStatus::Pass => "[ok]",
                        CheckStatus::Warn => "[warn]",
                        CheckStatus::Fail => "[fail]",
                    };
                    println!("{marker:<6} {:<16} {}", check.name, check.message);
                }
                let passes = report
                    .checks
                    .iter()
                    .filter(|c| matches!(c.status, CheckStatus::Pass))
                    .count();
                let warns = report
                    .checks
                    .iter()
                    .filter(|c| matches!(c.status, CheckStatus::Warn))
                    .count();
                let fails = report
                    .checks
                    .iter()
                    .filter(|c| matches!(c.status, CheckStatus::Fail))
                    .count();
                println!(
                    "\n{} checks passed, {} warnings, {} failures",
                    passes, warns, fails
                );

                if !report.next_steps.is_empty() {
                    println!("\nNext steps:");
                    for step in &report.next_steps {
                        println!("- {step}");
                    }
                }
            }
            if !ok {
                std::process::exit(1);
            }
        }
        Command::Setup { command } => match command {
            SetupCommand::Audit {
                repo: command_repo,
                markdown,
                write,
                exit_code,
            } => {
                let repo = resolve_repo(&repo, command_repo);
                let report = setup_audit_report(&repo);
                if markdown || write.is_some() {
                    let rendered = render_setup_audit_markdown(&report);
                    if let Some(path) = write {
                        fs::write(&path, rendered)?;
                        if cli.json {
                            println!(
                                "{}",
                                serde_json::to_string_pretty(&serde_json::json!({
                                    "ok": report.ok,
                                    "path": path,
                                }))?
                            );
                        } else {
                            println!("Wrote Open Kioku setup audit to {}", path.display());
                        }
                    } else {
                        println!("{rendered}");
                    }
                } else if cli.json {
                    println!("{}", serde_json::to_string_pretty(&report)?);
                } else {
                    print_setup_audit_report(&report);
                }
                if exit_code && !report.ok {
                    anyhow::bail!("Open Kioku setup audit has failing checks");
                }
            }
        },
        Command::Demo { path, force } => {
            let repo = demo_repo_path(path)?;
            let report = build_demo_repo(&repo, force)?;
            if cli.json {
                println!("{}", serde_json::to_string_pretty(&report)?);
            } else {
                println!("Demo repo ready: {}", report.repo.display());
                println!(
                    "Indexed {} files, {} symbols, {} chunks",
                    report.file_count, report.symbol_count, report.chunk_count
                );
                println!("\nTry:");
                for command in &report.commands {
                    println!("  {command}");
                }
            }
        }
        Command::Search { query, limit } => {
            let store = open_store(&repo)?;
            let results = search(&repo, &store, &query, limit)?;
            output(cli.json, &results, || {
                for result in &results {
                    println!(
                        "{}:{}  {:.2}  {}",
                        result.path.display(),
                        result.line_range.as_ref().map(|r| r.start).unwrap_or(0),
                        result.score,
                        result.snippet
                    );
                }
            })?;
        }
        Command::Symbol { command } => {
            let store = open_store(&repo)?;
            let engine = SymbolEngine::new(&store);
            match command {
                SymbolCommand::Find { name } => output(cli.json, &engine.find(&name, 50)?, || {})?,
                SymbolCommand::Definition { name } => {
                    output(cli.json, &engine.definition(&name)?, || {})?
                }
                SymbolCommand::Refs { name } => {
                    output(cli.json, &engine.references(&name, 50)?, || {})?
                }
            }
        }
        Command::Explain { command } => {
            let store = open_store(&repo)?;
            match command {
                ExplainCommand::File { path } => {
                    let file = store.get_file_by_path(&path)?;
                    let chunks = if let Some(file) = &file {
                        store.chunks_for_file(&file.id)?
                    } else {
                        Vec::new()
                    };
                    let symbols = if let Some(file) = &file {
                        store.symbols_for_file(&file.id)?
                    } else {
                        Vec::new()
                    };
                    output(
                        cli.json,
                        &serde_json::json!({"file": file, "chunks": chunks, "symbols": symbols}),
                        || {
                            if let Some(f) = &file {
                                println!(
                                    "{} ({:?}, {} bytes)",
                                    path.display(),
                                    f.language,
                                    f.size_bytes
                                );
                            }
                            println!("{} chunks, {} symbols indexed", chunks.len(), symbols.len());
                            for symbol in &symbols {
                                let range = symbol
                                    .range
                                    .as_ref()
                                    .map(|r| format!(":{}–{}", r.start, r.end))
                                    .unwrap_or_default();
                                println!("  {:?} {}{}", symbol.kind, symbol.name, range);
                            }
                        },
                    )?;
                }
                ExplainCommand::Symbol { name } => {
                    let symbol = SymbolEngine::new(&store).definition(&name)?;
                    output(cli.json, &symbol, || {})?;
                }
            }
        }
        Command::Impact(args) => {
            let store = open_store(&repo)?;
            let index_dir = default_index_dir(&repo);
            let search_index = if TantivySearchIndex::exists(&index_dir) {
                Some(TantivySearchIndex::open_or_create(&index_dir)?)
            } else {
                None
            };
            let engine = ImpactEngine::new(&store)
                .with_search_index(search_index.as_ref().map(|idx| idx as &dyn SearchIndex));

            let report = if let Some(path) = args.file {
                let normalized = normalize_to_repo_relative(&repo, &path);
                engine.for_file(&normalized)?
            } else if let Some(symbol) = args.symbol {
                let definition = SymbolEngine::new(&store).definition(&symbol)?;
                let files = store.list_files(usize::MAX, 0)?;
                let file = files.iter().find(|file| file.id == definition.file_id);
                let path_to_use = file
                    .map(|file| file.path.as_path())
                    .unwrap_or(Path::new(&symbol));
                let normalized = normalize_to_repo_relative(&repo, path_to_use);
                engine.for_file(&normalized)?
            } else {
                anyhow::bail!("provide --file or --symbol");
            };
            output(cli.json, &report, || {
                println!("Impact target: {}", report.target);
                println!(
                    "Risk: {} ({:.2})",
                    report.risk_report.level, report.risk_report.score
                );
                println!("\nDirect impacts ({}):", report.direct_impacts.len());
                for result in &report.direct_impacts {
                    println!(
                        "  {}:{} ({:.2})",
                        result.path.display(),
                        result.line_range.as_ref().map(|r| r.start).unwrap_or(0),
                        result.score
                    );
                }
                if !report.indirect_impacts.is_empty() {
                    println!("\nIndirect impacts ({}):", report.indirect_impacts.len());
                    for result in report.indirect_impacts.iter().take(5) {
                        println!(
                            "  {}:{} ({:.2})",
                            result.path.display(),
                            result.line_range.as_ref().map(|r| r.start).unwrap_or(0),
                            result.score
                        );
                    }
                }
            })?;
        }
        Command::Path { from, to } => {
            let store = open_store(&repo)?;
            let from = resolve_graph_node(&store, &from)?;
            let to = resolve_graph_node(&store, &to)?;
            let path = store.shortest_path(&from, &to, 12)?;
            output(cli.json, &path, || {
                if path.is_empty() {
                    println!("No dependency path found.");
                } else {
                    for edge in &path {
                        println!("{} -> {} {:?}", edge.from, edge.to, edge.edge_type);
                    }
                }
            })?;
        }
        Command::Tests { changed } => {
            let store = open_store(&repo)?;
            output(
                cli.json,
                &TestSelector::new(&store).for_changed_path_with_evidence(&changed, 20)?,
                || {},
            )?;
        }
        Command::Context {
            task,
            format,
            compressed,
        } => {
            let store = open_store(&repo)?;
            let pack = build_context_pack(&repo, &store, &task, 20)?;
            if compressed {
                let compressed = ContextHandleStore::open_repo(&repo)?.compress_pack(&pack)?;
                if cli.json || format == ContextPackFormat::Json {
                    println!("{}", serde_json::to_string_pretty(&compressed)?);
                } else if format == ContextPackFormat::Toon {
                    println!(
                        "{}",
                        open_kioku_format::render_compressed_context_toon(&compressed)
                    );
                } else {
                    println!("{}", serde_json::to_string_pretty(&compressed)?);
                }
            } else {
                let rendered = format.render(&pack)?;
                println!("{}", rendered);
            }
        }
        Command::RetrieveContext { handle } => {
            let retrieved =
                ContextHandleStore::open_repo(&repo)?.retrieve(&ContextHandleId::new(handle))?;
            output(cli.json, &retrieved, || {
                if let Some(retrieved) = &retrieved {
                    println!("{}", retrieved.original);
                } else {
                    println!("No context handle found.");
                }
            })?;
        }
        Command::Plan {
            task,
            format,
            limit,
        } => {
            let store = open_store(&repo)?;
            let context = build_context_pack(&repo, &store, &task, limit)?;
            let index_dir = default_index_dir(&repo);
            let search_index = if TantivySearchIndex::exists(&index_dir) {
                Some(TantivySearchIndex::open_or_create(&index_dir)?)
            } else {
                None
            };
            let report = PlanEngine::new(&store as &dyn OkStore)
                .with_search_index(search_index.as_ref().map(|idx| idx as &dyn SearchIndex))
                .with_memory_facts(RepoMemoryStore::open_repo(&repo)?.search(&task, 8)?)
                .plan_from_context(&task, limit, context)?;
            let format = if cli.json { PlanFormat::Json } else { format };
            println!("{}", format.render(&report)?);
        }
        Command::Bench(args) => {
            let min_precision = args.quality_min_precision_at_1;
            let report = run_bench(args)?;
            if cli.json {
                println!("{}", serde_json::to_string_pretty(&report)?);
            } else {
                print_bench_report(&report);
            }
            if let Some(quality) = &report.quality {
                if quality.precision_at_1 < min_precision {
                    anyhow::bail!(
                        "quality precision@1 {:.3} is below required {:.3}",
                        quality.precision_at_1,
                        min_precision
                    );
                }
            }
        }
        Command::Eval(args) => {
            let min_recall = args.min_recall_at_k;
            let min_mrr = args.min_mrr;
            let report = run_eval(args)?;
            if cli.json {
                println!("{}", serde_json::to_string_pretty(&report)?);
            } else {
                print_eval_report(&report);
            }
            if report.summary.search_recall_at_k < min_recall {
                anyhow::bail!(
                    "eval search recall@{} {:.3} is below required {:.3}",
                    report.limit,
                    report.summary.search_recall_at_k,
                    min_recall
                );
            }
            if report.summary.search_mrr < min_mrr {
                anyhow::bail!(
                    "eval MRR {:.3} is below required {:.3}",
                    report.summary.search_mrr,
                    min_mrr
                );
            }
        }
        Command::Prove(args) => {
            let format = if cli.json {
                ProveFormat::Json
            } else {
                args.format
            };
            let report = run_proof(args)?;
            if matches!(format, ProveFormat::Json) {
                println!("{}", serde_json::to_string_pretty(&report)?);
            } else {
                println!("{}", render_proof_markdown(&report));
            }
        }
        Command::Architecture { command } => {
            let store = open_store(&repo)?;
            let summary = ArchitectureDetector::new(&store).detect()?;
            match command {
                ArchitectureCommand::Detect => output(cli.json, &summary, || {})?,
                ArchitectureCommand::Boundaries => output(cli.json, &summary.components, || {})?,
                ArchitectureCommand::Violations => output(cli.json, &summary.violations, || {})?,
            }
        }
        Command::Patch { command } => {
            let config = OkConfig::load_from_repo(&repo)?;
            let store = open_store(&repo)?;
            let planner = PatchPlanner::new(&config, &store as &dyn OkStore);
            match command {
                PatchCommand::Plan { task } => output(cli.json, &planner.plan(&task)?, || {})?,
                PatchCommand::Review { id } => {
                    let response = serde_json::json!({
                        "id": id,
                        "status": "requires_stored_patch_plan",
                        "message": "patch review requires a stored patch plan"
                    });
                    print_text_or_json(
                        cli.json,
                        &format!("patch review requires stored patch plan id={id}"),
                        &response,
                    )?;
                }
                PatchCommand::Apply { id, approved } => {
                    anyhow::bail!("patch apply is policy gated and requires a stored diff; id={id} approved={approved}");
                }
            }
        }
        Command::Memory { command } => {
            let memory = RepoMemoryStore::open_repo(&repo)?;
            match command {
                MemoryCommand::Remember {
                    text,
                    source,
                    confidence,
                } => {
                    let fact = memory.remember(&text, &source, confidence.into())?;
                    output(cli.json, &fact, || {
                        println!(
                            "{}",
                            serde_json::to_string_pretty(&fact).unwrap_or_default()
                        );
                    })?;
                }
                MemoryCommand::Search { query, limit } => {
                    let results = memory.search(&query, limit)?;
                    output(cli.json, &results, || {
                        if results.is_empty() {
                            println!("No repo memory matched.");
                        } else {
                            for result in &results {
                                println!(
                                    "{:.2} {} [{}]",
                                    result.score, result.fact.text, result.fact.source
                                );
                            }
                        }
                    })?;
                }
                MemoryCommand::Recent { limit } => {
                    let facts = memory.recent(limit)?;
                    output(cli.json, &facts, || {
                        for fact in &facts {
                            println!("{} [{}]", fact.text, fact.source);
                        }
                    })?;
                }
            }
        }
        Command::Mcp { command } => match command {
            McpCommand::Install { client, repo } => {
                let repo = absolutize(&repo)?;
                let snippet = mcp_install_snippet(client, &repo);
                if cli.json {
                    println!("{}", serde_json::to_string_pretty(&snippet)?);
                } else {
                    println!("{}", snippet["instructions"].as_str().unwrap_or_default());
                    if let Some(config_text) = snippet["config_text"].as_str() {
                        println!("{config_text}");
                    } else if let Ok(config) = serde_json::to_string_pretty(&snippet["config"]) {
                        println!("{config}");
                    }
                }
            }
            McpCommand::Serve {
                repo,
                read_only,
                allow_write,
                approval_required,
                allow_command,
                deny_network,
                hide_experimental,
            } => {
                let mut config = OkConfig::load_from_repo(&repo)?;
                config.mcp.mode = if read_only && !allow_write {
                    "read-only".into()
                } else {
                    "write".into()
                };
                config.security.allow_write = allow_write;
                config.security.approval_required = approval_required;
                config.security.deny_network = deny_network;
                config.mcp.hide_experimental = hide_experimental;
                if !allow_command.is_empty() {
                    config.commands.allow = allow_command;
                }
                open_kioku_mcp::serve_stdio(repo, config).await?;
            }
        },
        Command::Scip { command } => match command {
            ScipCommand::Doctor { repo: command_repo } => {
                let repo = resolve_repo(&repo, command_repo);
                let config = OkConfig::load_from_repo(&repo)?;
                let snapshot = scip_setup_report(&repo, &config);
                if cli.json {
                    println!("{}", serde_json::to_string_pretty(&snapshot)?);
                } else {
                    print_scip_setup_report(&snapshot);
                }
            }
            ScipCommand::Setup { repo: command_repo } => {
                let repo = resolve_repo(&repo, command_repo);
                let config = OkConfig::load_from_repo(&repo)?;
                let snapshot = scip_setup_report(&repo, &config);
                if cli.json {
                    println!("{}", serde_json::to_string_pretty(&snapshot)?);
                } else {
                    print_scip_setup_report(&snapshot);
                    println!("\nTo generate where installed:");
                    println!(
                        "  ok index {} --with-scip auto",
                        shell_quote(&repo.display().to_string())
                    );
                    println!("\nOpen Kioku will never install SCIP indexers unless a future explicit install flag enables it.");
                }
            }
        },
    }
    Ok(())
}

fn load_index_manifest(repo: &Path) -> anyhow::Result<Option<IndexManifest>> {
    let index_path = repo.join(".ok/index.sqlite");
    if !index_path.exists() {
        return Ok(None);
    }
    Ok(SqliteStore::open(&index_path)?.manifest()?)
}

fn render_status_markdown(
    repo: &Path,
    manifest: Option<&IndexManifest>,
    doctor: &DoctorReport,
) -> String {
    let mut out = String::new();
    out.push_str("# Open Kioku Status\n\n");
    out.push_str("| Field | Value |\n| --- | --- |\n");
    out.push_str(&format!("| Repo | `{}` |\n", repo.display()));
    out.push_str(&format!("| Ready | `{}` |\n", doctor.ok));
    out.push_str("| Generated by | `ok status --markdown` |\n");

    out.push_str("\n## Index\n\n");
    if let Some(manifest) = manifest {
        out.push_str("| Metric | Value |\n| --- | ---: |\n");
        out.push_str(&format!("| Files | {} |\n", manifest.file_count));
        out.push_str(&format!("| Symbols | {} |\n", manifest.symbol_count));
        out.push_str(&format!("| Chunks | {} |\n", manifest.chunk_count));
        out.push_str(&format!("| Tests | {} |\n", manifest.quality.test_count));
        out.push_str(&format!(
            "| Imports | {} |\n",
            manifest.quality.import_count
        ));
        out.push_str(&format!(
            "| SCIP indexes imported | {} |\n",
            manifest.quality.scip_indexes_imported
        ));
        out.push_str(&format!(
            "| SCIP exact references | {} |\n",
            manifest.quality.scip_exact_references
        ));
        out.push_str(&format!(
            "| Static analysis facts | {} |\n",
            manifest.quality.static_analysis_facts
        ));
        if manifest.quality.runtime_analysis_facts > 0 {
            out.push_str(&format!(
                "| Runtime analysis facts | {} |\n",
                manifest.quality.runtime_analysis_facts
            ));
        }
        if manifest.quality.codeql_databases > 0 {
            out.push_str(&format!(
                "| CodeQL databases | {} |\n",
                manifest.quality.codeql_databases
            ));
        }
        if manifest.quality.coverage_reports > 0 {
            out.push_str(&format!(
                "| Coverage reports | {} |\n",
                manifest.quality.coverage_reports
            ));
        }
        if manifest.quality.junit_reports > 0 {
            out.push_str(&format!(
                "| JUnit reports | {} |\n",
                manifest.quality.junit_reports
            ));
        }
        out.push_str(&format!("\nIndexed at `{}`.\n", manifest.indexed_at));
        if !manifest.quality.build_systems.is_empty() {
            out.push_str(&format!(
                "\nBuild systems: `{}`.\n",
                manifest.quality.build_systems.join(", ")
            ));
        }
        if !manifest.quality.semantic_provider_notes.is_empty() {
            out.push_str("\nLocal signal notes:\n");
            for note in &manifest.quality.semantic_provider_notes {
                out.push_str(&format!("- {}\n", note));
            }
        }
        if !manifest.quality.quality_notes.is_empty() {
            out.push_str("\nQuality notes:\n");
            for note in &manifest.quality.quality_notes {
                out.push_str(&format!("- {}\n", note));
            }
        }
    } else {
        out.push_str(
            "No index manifest was found. Run `ok index .` before handing this repo to an agent.\n",
        );
    }

    out.push_str("\n## Readiness Checks\n\n");
    out.push_str("| Status | Check | Evidence |\n| --- | --- | --- |\n");
    for check in &doctor.checks {
        out.push_str(&format!(
            "| `{}` | `{}` | {} |\n",
            check.status.label(),
            check.name,
            markdown_cell(&check.message)
        ));
    }

    out.push_str("\n## Next Steps\n\n");
    if doctor.next_steps.is_empty() {
        out.push_str("- No required next steps.\n");
    } else {
        for step in &doctor.next_steps {
            out.push_str(&format!("- {step}\n"));
        }
    }

    out.push_str("\n## Handoff Commands\n\n");
    out.push_str(&format!(
        "- `ok setup audit --repo {}`\n",
        shell_quote(&repo.display().to_string())
    ));
    out.push_str(&format!(
        "- `ok prove {}`\n",
        shell_quote(&repo.display().to_string())
    ));
    out
}

fn setup_audit_report(repo: &Path) -> SetupAuditReport {
    let repo = absolutize(repo).unwrap_or_else(|_| repo.to_path_buf());
    let doctor = doctor_report(&repo);
    let manifest = load_index_manifest(&repo).ok().flatten();
    let config = OkConfig::load_from_repo(&repo).ok();
    let providers = quality_provider_report(&repo, manifest.as_ref());
    let advanced_providers = advanced_quality_provider_report(&repo, manifest.as_ref());
    let mut checks = Vec::new();
    let mut next_steps = doctor.next_steps.clone();

    if let Some(manifest) = &manifest {
        checks.push(SetupAuditCheck {
            name: "index".into(),
            status: CheckStatus::Pass,
            message: format!(
                "{} files, {} symbols, {} chunks",
                manifest.file_count, manifest.symbol_count, manifest.chunk_count
            ),
        });
        if manifest.quality.scip_exact_references > 0 {
            checks.push(SetupAuditCheck {
                name: "scip".into(),
                status: CheckStatus::Pass,
                message: format!(
                    "{} exact references imported",
                    manifest.quality.scip_exact_references
                ),
            });
        } else {
            checks.push(SetupAuditCheck {
                name: "scip".into(),
                status: CheckStatus::Warn,
                message:
                    "SCIP exact references are unavailable; impact and plan quality are reduced"
                        .into(),
            });
        }
    } else {
        checks.push(SetupAuditCheck {
            name: "index".into(),
            status: CheckStatus::Fail,
            message: "missing .ok/index.sqlite manifest".into(),
        });
        next_steps.push("Run `ok index .` before relying on Open Kioku in an agent.".into());
    }

    match config {
        Some(config) => {
            if !config.security.allow_write
                && config.security.deny_network
                && config.security.approval_required
            {
                checks.push(SetupAuditCheck {
                    name: "security".into(),
                    status: CheckStatus::Pass,
                    message: "read-only source access, network denied, approvals required".into(),
                });
            } else {
                checks.push(SetupAuditCheck {
                    name: "security".into(),
                    status: CheckStatus::Warn,
                    message: format!(
                        "allow_write={}, deny_network={}, approval_required={}",
                        config.security.allow_write,
                        config.security.deny_network,
                        config.security.approval_required
                    ),
                });
                next_steps.push(
                    "Review ok.toml before exposing write, command, or network access to agents."
                        .into(),
                );
            }
        }
        None => {
            checks.push(SetupAuditCheck {
                name: "config".into(),
                status: CheckStatus::Warn,
                message: "ok.toml is missing or invalid; defaults will be used".into(),
            });
            next_steps.push("Run `ok init .` to create an explicit ok.toml.".into());
        }
    }

    let mcp_check = doctor.checks.iter().find(|check| check.name == "mcp");
    checks.push(SetupAuditCheck {
        name: "mcp".into(),
        status: mcp_check
            .map(|check| check.status)
            .unwrap_or(CheckStatus::Warn),
        message: mcp_check
            .map(|check| check.message.clone())
            .unwrap_or_else(|| "MCP server check was not available".into()),
    });

    let plugin_surfaces = plugin_surfaces(&repo);

    next_steps.sort();
    next_steps.dedup();
    let ok = checks
        .iter()
        .all(|check| !matches!(check.status, CheckStatus::Fail));
    SetupAuditReport {
        ok,
        repo: repo.clone(),
        generated_by: "ok setup audit",
        checks,
        providers,
        advanced_providers,
        clients: all_mcp_clients()
            .into_iter()
            .map(|client| ClientInstallReport {
                client: client.as_str(),
                config_format: client.config_format(),
                install_command: format!(
                    "ok mcp install {} --repo {}",
                    client.as_str(),
                    shell_quote(&repo.display().to_string())
                ),
                verify: client_verify_command(client),
                note: client_install_note(client),
            })
            .collect(),
        plugin_surfaces,
        next_steps,
    }
}

fn print_setup_audit_report(report: &SetupAuditReport) {
    println!("Open Kioku setup audit for {}", report.repo.display());
    for check in &report.checks {
        println!(
            "{:<6} {:<12} {}",
            check.status.marker(),
            check.name,
            check.message
        );
    }
    println!("\nMCP clients:");
    for client in &report.clients {
        println!(
            "- {:<8} {:<5} {}",
            client.client, client.config_format, client.install_command
        );
    }
    println!("\nQuality signals:");
    for provider in &report.providers {
        println!(
            "{:<6} {:<12} {}",
            provider.status.marker(),
            provider.name,
            provider.evidence
        );
    }
    println!("\nAdvanced providers (optional):");
    if report.advanced_providers.is_empty() {
        println!("- none detected; not required for default SCIP/indexed-facts workflow");
    } else {
        for provider in &report.advanced_providers {
            println!(
                "{:<6} {:<12} {}",
                provider.status.marker(),
                provider.name,
                provider.evidence
            );
        }
    }
    println!("\nSource checkout surfaces (optional):");
    for surface in &report.plugin_surfaces {
        let status = if surface.present {
            "present"
        } else {
            "missing"
        };
        println!(
            "- {:<14} {:<7} {}",
            surface.name,
            status,
            surface.path.display()
        );
    }
    if !report.next_steps.is_empty() {
        println!("\nNext steps:");
        for step in &report.next_steps {
            println!("- {step}");
        }
    }
}

fn render_setup_audit_markdown(report: &SetupAuditReport) -> String {
    let mut out = String::new();
    out.push_str("# Open Kioku Setup Audit\n\n");
    out.push_str("| Field | Value |\n| --- | --- |\n");
    out.push_str(&format!("| Repo | `{}` |\n", report.repo.display()));
    out.push_str(&format!("| Ready | `{}` |\n", report.ok));
    out.push_str(&format!("| Generated by | `{}` |\n", report.generated_by));

    out.push_str("\n## Checks\n\n");
    out.push_str("| Status | Check | Evidence |\n| --- | --- | --- |\n");
    for check in &report.checks {
        out.push_str(&format!(
            "| `{}` | `{}` | {} |\n",
            check.status.label(),
            check.name,
            markdown_cell(&check.message)
        ));
    }

    out.push_str("\n## MCP Client Matrix\n\n");
    out.push_str("| Client | Config | Install command | Verify |\n| --- | --- | --- | --- |\n");
    for client in &report.clients {
        out.push_str(&format!(
            "| `{}` | `{}` | `{}` | `{}` |\n",
            client.client, client.config_format, client.install_command, client.verify
        ));
    }

    out.push_str("\n## Quality Signals\n\n");
    out.push_str("| Status | Signal | Evidence | Next step |\n| --- | --- | --- | --- |\n");
    for provider in &report.providers {
        out.push_str(&format!(
            "| `{}` | `{}` | {} | {} |\n",
            provider.status.label(),
            provider.name,
            markdown_cell(&provider.evidence),
            markdown_cell(provider.next_step.as_deref().unwrap_or("None"))
        ));
    }

    out.push_str("\n## Advanced Providers\n\n");
    out.push_str("Optional only. Missing entries do not reduce default readiness; Open Kioku's primary precision path is local indexed facts plus SCIP when available.\n\n");
    if report.advanced_providers.is_empty() {
        out.push_str("No advanced provider artifacts detected.\n");
    } else {
        out.push_str("| Status | Provider | Evidence | Next step |\n| --- | --- | --- | --- |\n");
        for provider in &report.advanced_providers {
            out.push_str(&format!(
                "| `{}` | `{}` | {} | {} |\n",
                provider.status.label(),
                provider.name,
                markdown_cell(&provider.evidence),
                markdown_cell(provider.next_step.as_deref().unwrap_or("None"))
            ));
        }
    }

    out.push_str("\n## Source Checkout Surfaces\n\n");
    out.push_str("These are expected only when auditing the Open Kioku source checkout, not every indexed target repository.\n\n");
    out.push_str("| Surface | Status | Path | Note |\n| --- | --- | --- | --- |\n");
    for surface in &report.plugin_surfaces {
        out.push_str(&format!(
            "| `{}` | `{}` | `{}` | {} |\n",
            surface.name,
            if surface.present {
                "present"
            } else {
                "missing"
            },
            surface.path.display(),
            surface.note
        ));
    }

    out.push_str("\n## Next Steps\n\n");
    if report.next_steps.is_empty() {
        out.push_str("- No required next steps.\n");
    } else {
        for step in &report.next_steps {
            out.push_str(&format!("- {step}\n"));
        }
    }
    out
}

fn markdown_cell(value: &str) -> String {
    value.replace('|', "\\|").replace('\n', " ")
}

fn all_mcp_clients() -> [McpClient; 6] {
    [
        McpClient::Claude,
        McpClient::Cursor,
        McpClient::Codex,
        McpClient::Gemini,
        McpClient::Opencode,
        McpClient::Zed,
    ]
}

fn client_verify_command(client: McpClient) -> String {
    match client {
        McpClient::Claude => "restart Claude, then inspect MCP server logs".into(),
        McpClient::Cursor => "open Cursor MCP settings and confirm open-kioku is enabled".into(),
        McpClient::Codex => "run /mcp in Codex and confirm open-kioku is listed".into(),
        McpClient::Gemini => "run gemini /mcp and confirm open-kioku is connected".into(),
        McpClient::Opencode => "run opencode and ask it to use the open-kioku MCP tools".into(),
        McpClient::Zed => "open Agent Panel settings and confirm the server is active".into(),
    }
}

fn client_install_note(client: McpClient) -> &'static str {
    match client {
        McpClient::Claude => "Claude-style mcpServers JSON.",
        McpClient::Cursor => "Cursor MCP JSON entry.",
        McpClient::Codex => "Codex config.toml mcp_servers entry.",
        McpClient::Gemini => "Gemini CLI settings.json mcpServers entry.",
        McpClient::Opencode => "OpenCode opencode.json mcp local server entry.",
        McpClient::Zed => "Zed settings.json context_servers entry.",
    }
}

fn plugin_surfaces(repo: &Path) -> Vec<PluginSurfaceReport> {
    vec![
        PluginSurfaceReport {
            name: "cursor-plugin",
            path: repo.join(".cursor-plugin/plugin.json"),
            present: repo.join(".cursor-plugin/plugin.json").exists(),
            note: "Cursor plugin manifest.",
        },
        PluginSurfaceReport {
            name: "claude-plugin",
            path: repo.join(".claude-plugin/plugin.json"),
            present: repo.join(".claude-plugin/plugin.json").exists(),
            note: "Claude plugin manifest.",
        },
        PluginSurfaceReport {
            name: "github-workflows",
            path: repo.join(".github/workflows"),
            present: repo.join(".github/workflows").is_dir(),
            note: "CI and release automation.",
        },
    ]
}

fn quality_provider_report(
    repo: &Path,
    manifest: Option<&IndexManifest>,
) -> Vec<QualityProviderReport> {
    let build_systems = detect_build_systems(repo);
    let test_count = manifest
        .map(|manifest| manifest.quality.test_count)
        .unwrap_or(0);
    let import_count = manifest
        .map(|manifest| manifest.quality.import_count)
        .unwrap_or(0);
    let static_analysis_facts = manifest
        .map(|manifest| manifest.quality.static_analysis_facts)
        .unwrap_or(0);
    let runtime_analysis_facts = manifest
        .map(|manifest| manifest.quality.runtime_analysis_facts)
        .unwrap_or(0);
    let mut providers = Vec::new();

    providers.push(QualityProviderReport {
        name: "build",
        status: if build_systems.is_empty() {
            CheckStatus::Warn
        } else {
            CheckStatus::Pass
        },
        evidence: if build_systems.is_empty() {
            "no build system files detected".into()
        } else {
            format!("detected {}", build_systems.join(", "))
        },
        next_step: if build_systems.is_empty() {
            Some("Run from the repository root or add ok.toml with the intended root.".into())
        } else {
            None
        },
    });
    providers.push(QualityProviderReport {
        name: "tests",
        status: if test_count > 0 {
            CheckStatus::Pass
        } else {
            CheckStatus::Warn
        },
        evidence: format!("{test_count} indexed test target(s)"),
        next_step: if test_count == 0 {
            Some("Index test files before relying on validation recommendations.".into())
        } else {
            None
        },
    });
    providers.push(QualityProviderReport {
        name: "imports",
        status: if import_count > 0 {
            CheckStatus::Pass
        } else {
            CheckStatus::Warn
        },
        evidence: format!("{import_count} indexed import edge(s)"),
        next_step: if import_count == 0 {
            Some("Index source files with imports to improve local dependency evidence.".into())
        } else {
            None
        },
    });
    providers.push(QualityProviderReport {
        name: "static",
        status: if manifest.is_some() {
            CheckStatus::Pass
        } else {
            CheckStatus::Warn
        },
        evidence: format!("{static_analysis_facts} language-specific static analysis fact(s)"),
        next_step: if manifest.is_none() {
            Some("Run `ok index .` to collect language-specific static analysis facts.".into())
        } else {
            None
        },
    });
    if runtime_analysis_facts > 0 {
        providers.push(QualityProviderReport {
            name: "runtime",
            status: CheckStatus::Pass,
            evidence: format!(
                "{runtime_analysis_facts} runtime analysis fact(s) from local artifacts"
            ),
            next_step: None,
        });
    }
    providers.push(QualityProviderReport {
        name: "validation",
        status: if test_count > 0 {
            CheckStatus::Pass
        } else {
            CheckStatus::Warn
        },
        evidence: if build_systems.iter().any(|system| system == "gradle") && test_count > 0 {
            "Gradle-scoped validation commands enabled for indexed Java test paths".into()
        } else if test_count > 0 {
            "indexed validation candidates available".into()
        } else {
            "no indexed validation candidates".into()
        },
        next_step: if test_count == 0 {
            Some("Add or index tests so plans can return concrete validation commands.".into())
        } else {
            None
        },
    });
    providers
}

fn advanced_quality_provider_report(
    repo: &Path,
    manifest: Option<&IndexManifest>,
) -> Vec<QualityProviderReport> {
    let codeql_dbs = detect_codeql_databases(repo);
    let bsp_descriptors = count_named_artifacts(&[repo.join(".bsp")], &[".json"], 2);
    let coverage_reports = manifest
        .map(|manifest| manifest.quality.coverage_reports)
        .unwrap_or_else(|| {
            count_named_artifacts(&analysis_roots(repo), &["jacoco.xml", "coverage.xml"], 5)
        });
    let junit_reports = manifest
        .map(|manifest| manifest.quality.junit_reports)
        .unwrap_or_else(|| count_named_artifacts(&analysis_roots(repo), &["test-", "junit"], 5));
    let lsp = relevant_lsp_servers(repo);
    let mut providers = Vec::new();

    if bsp_descriptors > 0 {
        providers.push(QualityProviderReport {
            name: "bsp",
            status: CheckStatus::Pass,
            evidence: format!("{bsp_descriptors} BSP descriptor(s) under .bsp"),
            next_step: None,
        });
    }
    if codeql_dbs > 0 {
        providers.push(QualityProviderReport {
            name: "codeql",
            status: CheckStatus::Pass,
            evidence: format!("{codeql_dbs} local CodeQL database artifact(s) detected"),
            next_step: None,
        });
    }
    if !lsp.present.is_empty() && lsp.missing.is_empty() {
        providers.push(QualityProviderReport {
            name: "lsp",
            status: CheckStatus::Pass,
            evidence: format!(
                "detected matching language servers: {}",
                lsp.present.join(", ")
            ),
            next_step: None,
        });
    }
    if coverage_reports > 0 {
        providers.push(QualityProviderReport {
            name: "coverage",
            status: CheckStatus::Pass,
            evidence: format!("{coverage_reports} coverage report artifact(s) detected"),
            next_step: None,
        });
    }
    if junit_reports > 0 {
        providers.push(QualityProviderReport {
            name: "junit",
            status: CheckStatus::Pass,
            evidence: format!("{junit_reports} JUnit-style report artifact(s) detected"),
            next_step: None,
        });
    }
    providers
}

fn detect_build_systems(repo: &Path) -> Vec<String> {
    let mut systems = Vec::new();
    for (name, paths) in [
        (
            "gradle",
            &[
                "settings.gradle",
                "settings.gradle.kts",
                "build.gradle",
                "build.gradle.kts",
            ][..],
        ),
        ("maven", &["pom.xml"][..]),
        (
            "bazel",
            &["WORKSPACE", "WORKSPACE.bazel", "MODULE.bazel"][..],
        ),
        ("cargo", &["Cargo.toml"][..]),
        ("npm", &["package.json"][..]),
        ("go", &["go.mod"][..]),
    ] {
        if paths.iter().any(|path| repo.join(path).exists()) {
            systems.push(name.to_string());
        }
    }
    systems
}

fn detect_codeql_databases(repo: &Path) -> usize {
    [
        ".ok/codeql",
        "codeql-db",
        "codeql-database",
        ".codeql/database",
    ]
    .iter()
    .filter(|path| {
        let path = repo.join(path);
        path.is_dir()
            && (path.join("db-java").exists()
                || path.join("codeql-database.yml").exists()
                || path.join("log").exists())
    })
    .count()
}

fn analysis_roots(repo: &Path) -> Vec<PathBuf> {
    vec![
        repo.join(".ok/analysis"),
        repo.join("build/reports"),
        repo.join("target/site"),
        repo.join("coverage"),
    ]
}

fn count_named_artifacts(roots: &[PathBuf], needles: &[&str], max_depth: usize) -> usize {
    let mut count = 0;
    for root in roots {
        if !root.is_dir() {
            continue;
        }
        for entry in walkdir::WalkDir::new(root)
            .max_depth(max_depth)
            .into_iter()
            .filter_map(|entry| entry.ok())
        {
            if !entry.file_type().is_file() {
                continue;
            }
            let path = entry.path().to_string_lossy().to_ascii_lowercase();
            let file_name = entry.file_name().to_string_lossy().to_ascii_lowercase();
            if needles
                .iter()
                .any(|needle| file_name.contains(needle) || path.ends_with(needle))
            {
                count += 1;
            }
        }
    }
    count
}

struct LspProviderInventory {
    present: Vec<String>,
    missing: Vec<String>,
}

fn relevant_lsp_servers(repo: &Path) -> LspProviderInventory {
    let languages = sample_lsp_languages(repo);
    let mut present = Vec::new();
    let mut missing = Vec::new();
    for language in &languages {
        let candidates: &[&str] = match language.as_str() {
            "java" => &["jdtls", "java-language-server"],
            "rust" => &["rust-analyzer"],
            "go" => &["gopls"],
            "python" => &["pyright-langserver", "pylsp"],
            "typescript" | "javascript" => &["typescript-language-server"],
            _ => &[],
        };
        if candidates.is_empty() {
            continue;
        }
        if let Some(found) = candidates.iter().find(|binary| command_exists(binary)) {
            present.push(format!("{language}:{found}"));
        } else {
            missing.push(format!("{} ({})", language, candidates.join(" or ")));
        }
    }
    present.sort();
    present.dedup();
    missing.sort();
    missing.dedup();
    LspProviderInventory { present, missing }
}

fn sample_lsp_languages(repo: &Path) -> Vec<String> {
    let mut languages = Vec::new();
    for entry in walkdir::WalkDir::new(repo)
        .max_depth(6)
        .into_iter()
        .filter_entry(|entry| {
            let name = entry.file_name().to_string_lossy();
            name != ".git"
                && name != ".ok"
                && name != "build"
                && name != "target"
                && name != "node_modules"
        })
        .filter_map(|entry| entry.ok())
        .take(5000)
    {
        if !entry.file_type().is_file() {
            continue;
        }
        let Some(ext) = entry.path().extension().and_then(|ext| ext.to_str()) else {
            continue;
        };
        let language = match ext {
            "java" => "java",
            "rs" => "rust",
            "go" => "go",
            "py" => "python",
            "ts" | "tsx" => "typescript",
            "js" | "jsx" => "javascript",
            _ => continue,
        };
        if !languages.iter().any(|existing| existing == language) {
            languages.push(language.to_string());
        }
    }
    languages.sort();
    languages
}

fn doctor_report(repo: &Path) -> DoctorReport {
    let repo = absolutize(repo).unwrap_or_else(|_| repo.to_path_buf());
    let mut checks = Vec::new();
    let mut next_steps = Vec::new();

    // 1. Rust toolchain version
    match std::process::Command::new("rustc")
        .arg("--version")
        .output()
    {
        Ok(output) if output.status.success() => {
            let version_str = String::from_utf8_lossy(&output.stdout);
            let version = version_str.split_whitespace().nth(1).unwrap_or("");
            if let Some(minor) = version
                .split('.')
                .nth(1)
                .and_then(|s| s.parse::<u32>().ok())
            {
                if minor < 75 {
                    checks.push(DoctorCheck {
                        name: "rustc",
                        status: CheckStatus::Warn,
                        message: format!("found rustc {version}, recommend >= 1.75"),
                    });
                } else {
                    checks.push(DoctorCheck {
                        name: "rustc",
                        status: CheckStatus::Pass,
                        message: format!("found rustc {version}"),
                    });
                }
            } else {
                checks.push(DoctorCheck {
                    name: "rustc",
                    status: CheckStatus::Pass,
                    message: format!("found {version_str}"),
                });
            }
        }
        _ => {
            checks.push(DoctorCheck {
                name: "rustc",
                status: CheckStatus::Warn,
                message: "rustc not found in PATH".into(),
            });
        }
    }

    // 2. .ok/ directory
    let ok_dir = repo.join(".ok");
    if ok_dir.is_dir() {
        checks.push(DoctorCheck {
            name: "repo",
            status: CheckStatus::Pass,
            message: format!("found .ok directory at {}", ok_dir.display()),
        });
    } else {
        checks.push(DoctorCheck {
            name: "repo",
            status: CheckStatus::Fail,
            message: format!(".ok directory missing at {}", ok_dir.display()),
        });
        next_steps.push("Run `ok init .` to create the configuration and data directory.".into());
    }

    // 3. .ok/index.sqlite
    let index_path = repo.join(".ok/index.sqlite");
    if index_path.exists() {
        match SqliteStore::open(&index_path).and_then(|store| store.manifest()) {
            Ok(Some(manifest)) => checks.push(DoctorCheck {
                name: "index",
                status: CheckStatus::Pass,
                message: format!(
                    "{} files, {} symbols, indexed at {}",
                    manifest.file_count, manifest.symbol_count, manifest.indexed_at
                ),
            }),
            Ok(None) => {
                checks.push(DoctorCheck {
                    name: "index",
                    status: CheckStatus::Warn,
                    message: "index database exists but has no manifest".into(),
                });
                next_steps.push("Run `ok index .` to build a fresh index.".into());
            }
            Err(err) => {
                checks.push(DoctorCheck {
                    name: "index",
                    status: CheckStatus::Fail,
                    message: err.to_string(),
                });
                next_steps.push("Remove .ok/index.sqlite and run `ok index .` again.".into());
            }
        }
    } else {
        checks.push(DoctorCheck {
            name: "index",
            status: CheckStatus::Fail,
            message: ".ok/index.sqlite is missing".into(),
        });
        next_steps.push("Run `ok index .` before connecting an MCP client.".into());
    }

    if index_path.exists() {
        if let Ok(store) = SqliteStore::open(&index_path) {
            if let Ok(Some(manifest)) = store.manifest() {
                let quality = &manifest.quality;
                if quality.scip_indexes_imported > 0 && quality.scip_exact_references > 0 {
                    checks.push(DoctorCheck {
                        name: "quality",
                        status: CheckStatus::Pass,
                        message: format!(
                            "SCIP imported {} index(es), {} exact references, {} tests",
                            quality.scip_indexes_imported,
                            quality.scip_exact_references,
                            quality.test_count
                        ),
                    });
                } else {
                    checks.push(DoctorCheck {
                        name: "quality",
                        status: CheckStatus::Warn,
                        message: format!(
                            "SCIP exact references unavailable; {} tests, {} imports indexed",
                            quality.test_count, quality.import_count
                        ),
                    });
                    next_steps.push(
                    "For better references, impact, tests, and planning: run `ok scip setup .`, then `ok index . --with-scip auto`.".into(),
                );
                }
            }
        }
    }

    // 4. ok.toml
    let config_path = repo.join("ok.toml");
    if config_path.exists() {
        match OkConfig::load_from_repo(&repo) {
            Ok(_) => checks.push(DoctorCheck {
                name: "config",
                status: CheckStatus::Pass,
                message: format!("loaded {}", config_path.display()),
            }),
            Err(err) => {
                checks.push(DoctorCheck {
                    name: "config",
                    status: CheckStatus::Fail,
                    message: err.to_string(),
                });
                next_steps.push("Fix ok.toml or regenerate it with `ok init .`.".into());
            }
        }
    } else {
        checks.push(DoctorCheck {
            name: "config",
            status: CheckStatus::Warn,
            message: "ok.toml is missing; defaults will be used".into(),
        });
        next_steps.push("Run `ok init .` to create ok.toml.".into());
    }

    // 5. Tree-sitter grammars
    let mut detected_languages = Vec::new();
    let walker = walkdir::WalkDir::new(&repo).into_iter().filter_entry(|e| {
        let name = e.file_name().to_string_lossy();
        name != ".ok" && name != "node_modules" && name != "target"
    });
    for entry in walker.filter_map(|e| e.ok()) {
        if entry.file_type().is_file() {
            let path = entry.path();
            if let Some(ext) = path.extension().and_then(|s| s.to_str()) {
                match ext {
                    "rs" => detected_languages.push("Rust"),
                    "ts" | "tsx" => detected_languages.push("TypeScript"),
                    "py" => detected_languages.push("Python"),
                    "go" => detected_languages.push("Go"),
                    "java" => detected_languages.push("Java"),
                    "js" | "jsx" => detected_languages.push("JavaScript"),
                    _ => {}
                }
            }
        }
    }
    detected_languages.sort();
    detected_languages.dedup();
    if detected_languages.is_empty() {
        checks.push(DoctorCheck {
            name: "grammars",
            status: CheckStatus::Pass,
            message: "no known source files detected".into(),
        });
    } else {
        checks.push(DoctorCheck {
            name: "grammars",
            status: CheckStatus::Pass,
            message: format!("parsers available for {}", detected_languages.join(", ")),
        });
    }

    // 6. MCP server check
    if let Ok(exe) = std::env::current_exe() {
        use std::io::Write;
        use std::process::{Command, Stdio};
        let child = Command::new(&exe)
            .args(["mcp", "serve", "--repo", repo.to_str().unwrap_or(".")])
            .stdin(Stdio::piped())
            .stdout(Stdio::piped())
            .stderr(Stdio::null())
            .spawn();

        if let Ok(mut child_proc) = child {
            let request = r#"{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05"}}"#;
            if let Some(mut stdin) = child_proc.stdin.take() {
                let _ = writeln!(stdin, "{}", request);
            }
            let mut result_buf = String::new();
            if let Some(stdout) = child_proc.stdout.take() {
                use std::io::BufRead;
                let mut reader = std::io::BufReader::new(stdout);
                let _ = reader.read_line(&mut result_buf);
            }
            let _ = child_proc.kill();

            if result_buf.contains("\"name\":\"open-kioku\"") {
                checks.push(DoctorCheck {
                    name: "mcp",
                    status: CheckStatus::Pass,
                    message: "server responded to initialize request".into(),
                });
            } else {
                checks.push(DoctorCheck {
                    name: "mcp",
                    status: CheckStatus::Fail,
                    message: "server failed to respond correctly".into(),
                });
            }
        } else {
            checks.push(DoctorCheck {
                name: "mcp",
                status: CheckStatus::Fail,
                message: "failed to spawn mcp server process".into(),
            });
        }
    } else {
        checks.push(DoctorCheck {
            name: "mcp",
            status: CheckStatus::Warn,
            message: "could not determine current executable to test server".into(),
        });
    }

    next_steps.dedup();
    let ok = checks
        .iter()
        .all(|check| !matches!(check.status, CheckStatus::Fail));
    DoctorReport {
        ok,
        repo,
        checks,
        next_steps,
    }
}

fn scip_setup_report(repo: &Path, config: &OkConfig) -> ScipSetupReport {
    let repo = absolutize(repo).unwrap_or_else(|_| repo.to_path_buf());
    let ts_args = if repo.join("tsconfig.json").exists() || repo.join("jsconfig.json").exists() {
        "scip-typescript index --output .ok/indexes/typescript.scip"
    } else {
        "scip-typescript index --output .ok/indexes/typescript.scip --infer-tsconfig"
    };
    let indexers = vec![
        ScipIndexerReport {
            language: "typescript/javascript",
            applicable: repo.join("package.json").exists(),
            installed: command_exists("scip-typescript"),
            command: ts_args.into(),
            output_path: ".ok/indexes/typescript.scip".into(),
            note: "best for TypeScript and JavaScript symbol references".into(),
        },
        ScipIndexerReport {
            language: "go",
            applicable: repo.join("go.mod").exists(),
            installed: command_exists("scip-go"),
            command: "scip-go".into(),
            output_path: "index.scip".into(),
            note: "best for Go definition/reference precision".into(),
        },
        ScipIndexerReport {
            language: "java",
            applicable: repo.join("pom.xml").exists()
                || repo.join("build.gradle").exists()
                || repo.join("build.gradle.kts").exists(),
            installed: command_exists("scip-java"),
            command: "scip-java index --output .ok/indexes/java.scip".into(),
            output_path: ".ok/indexes/java.scip".into(),
            note: "may run build-tool analysis and can take time".into(),
        },
        ScipIndexerReport {
            language: "python",
            applicable: repo.join("pyproject.toml").exists() || repo.join("setup.py").exists(),
            installed: command_exists("scip-python"),
            command: "scip-python index . --project-name <repo> --project-version _ --output .ok/indexes/python.scip".into(),
            output_path: ".ok/indexes/python.scip".into(),
            note: "requires project metadata for best external reference stability".into(),
        },
    ];
    ScipSetupReport {
        repo,
        mode: format!("{:?}", config.scip.mode).to_ascii_lowercase(),
        enabled: config.scip.enabled,
        allow_install: config.scip.allow_install,
        timeout_seconds: config.scip.timeout_seconds,
        indexers,
        configured_paths: config.scip.paths.clone(),
    }
}

fn print_scip_setup_report(report: &ScipSetupReport) {
    println!("SCIP setup for {}", report.repo.display());
    println!(
        "mode={}, enabled={}, timeout={}s",
        report.mode, report.enabled, report.timeout_seconds
    );
    println!("\nConfigured SCIP paths:");
    for path in &report.configured_paths {
        println!("- {}", path.display());
    }
    println!("\nIndexers:");
    for indexer in &report.indexers {
        let applicability = if indexer.applicable {
            "applicable"
        } else {
            "not detected"
        };
        let installed = if indexer.installed {
            "installed"
        } else {
            "missing"
        };
        println!(
            "- {}: {}, {}; {}",
            indexer.language, applicability, installed, indexer.note
        );
        if indexer.applicable {
            println!("  {}", indexer.command);
        }
    }
}

fn command_exists(binary: &str) -> bool {
    std::env::var_os("PATH")
        .map(|paths| {
            std::env::split_paths(&paths)
                .map(|dir| dir.join(binary))
                .any(|path| path.is_file())
        })
        .unwrap_or(false)
}

fn demo_repo_path(path: Option<PathBuf>) -> anyhow::Result<PathBuf> {
    match path {
        Some(path) => absolutize(&path),
        None => Ok(std::env::current_dir()?.join("open-kioku-demo")),
    }
}

fn build_demo_repo(repo: &Path, force: bool) -> anyhow::Result<DemoReport> {
    if repo.exists() {
        if !force {
            anyhow::bail!(
                "{} already exists; pass --force to replace the demo repo",
                repo.display()
            );
        }
        fs::remove_dir_all(repo)?;
    }

    fs::create_dir_all(repo.join("src"))?;
    fs::create_dir_all(repo.join("tests"))?;
    fs::write(
        repo.join("README.md"),
        "# Open Kioku Demo\n\nSmall repo for trying code search, symbols, impact, and MCP setup.\n",
    )?;
    fs::write(
        repo.join("Cargo.toml"),
        r#"[package]
name = "open-kioku-demo"
version = "0.1.0"
edition = "2021"
"#,
    )?;
    fs::write(
        repo.join("src/lib.rs"),
        r#"pub mod auth;

pub struct RequestContext {
    pub user_id: String,
}

pub fn handle_login(user_id: &str) -> String {
    let context = RequestContext {
        user_id: user_id.to_string(),
    };
    auth::issue_token(&context, 3600)
}
"#,
    )?;
    fs::write(
        repo.join("src/auth.rs"),
        r#"use crate::RequestContext;

pub fn issue_token(context: &RequestContext, ttl_seconds: u64) -> String {
    format!("token:{}:{}", context.user_id, ttl_seconds)
}

pub fn validate_token(token: &str) -> bool {
    token.starts_with("token:")
}

#[cfg(test)]
mod tests {
    use super::*;
    use crate::RequestContext;

    #[test]
    fn issues_token_with_user_id() {
        let context = RequestContext {
            user_id: "demo-user".into(),
        };
        assert!(issue_token(&context, 60).contains("demo-user"));
    }
}
"#,
    )?;
    fs::write(
        repo.join("tests/auth_flow.rs"),
        r#"use open_kioku_demo::{auth, handle_login};

#[test]
fn login_returns_valid_token() {
    let token = handle_login("demo-user");
    assert!(auth::validate_token(&token));
}
"#,
    )?;
    OkConfig::write_default(repo.join("ok.toml"))?;

    let snapshot = index_repo(repo)?;
    let repo_display = repo.display().to_string();
    Ok(DemoReport {
        repo: repo.to_path_buf(),
        file_count: snapshot.manifest.file_count,
        symbol_count: snapshot.manifest.symbol_count,
        chunk_count: snapshot.manifest.chunk_count,
        commands: vec![
            format!("ok --repo {repo_display} search token"),
            format!("ok --repo {repo_display} symbol find issue_token"),
            format!("ok --repo {repo_display} impact --file src/auth.rs"),
            format!("ok --repo {repo_display} context token --format markdown"),
            format!("ok --repo {repo_display} plan token --format markdown"),
            format!("ok prove {repo_display} --task token"),
            format!("ok mcp install claude --repo {repo_display}"),
        ],
    })
}

fn run_bench(args: BenchArgs) -> anyhow::Result<BenchReport> {
    let path = args.path;
    let quality_cases = parse_quality_cases(&args.quality_cases)?;

    let start = Instant::now();
    let snapshot = index_repo(&path)?;
    let index_duration = start.elapsed();

    let index = TantivySearchIndex::open_or_create(default_index_dir(&path))?;
    let bm25_median = median_duration(time_searches(10, || index.search("fn", 10).map(|_| ()))?);

    let store = open_store(&path)?;
    let files = store.list_files(usize::MAX, 0)?;
    let chunks = store.all_chunks()?;
    let symbols = store.list_symbols(None, usize::MAX, 0)?;
    let regex_median = median_duration(time_searches(10, || {
        search_chunks(&chunks, &files, &symbols, "fn", 10).map(|_| ())
    })?);

    let quality = if quality_cases.is_empty() {
        None
    } else {
        Some(evaluate_quality_cases(
            &index,
            &quality_cases,
            args.quality_limit,
        )?)
    };
    let manifest = snapshot.manifest;
    let elapsed_seconds = index_duration.as_secs_f64();

    Ok(BenchReport {
        repo: path,
        index: IndexBenchReport {
            file_count: manifest.file_count,
            symbol_count: manifest.symbol_count,
            chunk_count: manifest.chunk_count,
            elapsed_ms: duration_ms(index_duration),
            files_per_second: if elapsed_seconds > 0.0 {
                manifest.file_count as f64 / elapsed_seconds
            } else {
                0.0
            },
        },
        search: SearchBenchReport {
            bm25_median_ms: duration_ms(bm25_median),
            regex_median_ms: duration_ms(regex_median),
        },
        quality,
    })
}

fn parse_quality_cases(values: &[String]) -> anyhow::Result<Vec<QualityCase>> {
    values
        .iter()
        .map(|value| {
            let (query, expected_path) = value.split_once('=').ok_or_else(|| {
                anyhow::anyhow!("quality case must use QUERY=EXPECTED_PATH_SUBSTRING: {value}")
            })?;
            let query = query.trim();
            let expected_path = expected_path.trim();
            if query.is_empty() || expected_path.is_empty() {
                anyhow::bail!("quality case query and expected path must be non-empty: {value}");
            }
            Ok(QualityCase {
                query: query.to_string(),
                expected_path: expected_path.to_string(),
            })
        })
        .collect()
}

fn evaluate_quality_cases(
    index: &TantivySearchIndex,
    cases: &[QualityCase],
    limit: usize,
) -> anyhow::Result<QualityBenchReport> {
    let limit = limit.max(1);
    let mut reports = Vec::with_capacity(cases.len());
    let mut top_hits = 0usize;
    let mut any_hits = 0usize;
    let mut reciprocal_rank = 0.0;

    for case in cases {
        let results = index.search(&case.query, limit)?;
        let expected = normalize_path_fragment(&case.expected_path);
        let rank = results.iter().position(|result| {
            normalize_path_fragment(&result.path.to_string_lossy()).contains(&expected)
        });
        let rank = rank.map(|value| value + 1);
        if rank == Some(1) {
            top_hits += 1;
        }
        if let Some(rank) = rank {
            any_hits += 1;
            reciprocal_rank += 1.0 / rank as f64;
        }
        reports.push(QualityCaseReport {
            query: case.query.clone(),
            expected_path: case.expected_path.clone(),
            rank,
            top_path: results.first().map(|result| result.path.clone()),
            matched_path: rank
                .and_then(|rank| results.get(rank - 1).map(|result| result.path.clone())),
            result_count: results.len(),
        });
    }

    let total = cases.len() as f64;
    Ok(QualityBenchReport {
        case_count: cases.len(),
        precision_at_1: top_hits as f64 / total,
        hit_rate_at_k: any_hits as f64 / total,
        mean_reciprocal_rank: reciprocal_rank / total,
        limit,
        cases: reports,
    })
}

fn print_bench_report(report: &BenchReport) {
    println!(
        "Indexed {} files, {} symbols, and {} chunks in {:.2}ms",
        report.index.file_count,
        report.index.symbol_count,
        report.index.chunk_count,
        report.index.elapsed_ms
    );
    println!("{:.2} files/sec", report.index.files_per_second);
    println!("BM25 search: {:.2}ms median", report.search.bm25_median_ms);
    println!(
        "Regex search: {:.2}ms median",
        report.search.regex_median_ms
    );

    if let Some(quality) = &report.quality {
        println!(
            "Quality: precision@1 {:.3}, hit-rate@{} {:.3}, MRR {:.3}",
            quality.precision_at_1,
            quality.limit,
            quality.hit_rate_at_k,
            quality.mean_reciprocal_rank
        );
        for case in &quality.cases {
            let status = match case.rank {
                Some(1) => "pass",
                Some(_) => "hit",
                None => "miss",
            };
            let rank = case
                .rank
                .map(|rank| rank.to_string())
                .unwrap_or_else(|| "-".to_string());
            let top_path = case
                .top_path
                .as_ref()
                .map(|path| path.display().to_string())
                .unwrap_or_else(|| "-".to_string());
            println!(
                "  {status}: query {:?}, expected {:?}, rank {}, top {}",
                case.query, case.expected_path, rank, top_path
            );
        }
    }
}

fn run_eval(args: EvalArgs) -> anyhow::Result<EvalReport> {
    let repo = absolutize(&args.path)?;
    let limit = args.limit.clamp(1, 100);
    let cases = load_eval_cases(&args.cases, args.cases_file.as_ref())?;
    if cases.is_empty() {
        anyhow::bail!("no eval cases provided; pass --case TASK=EXPECTED_PATH or --cases-file");
    }

    index_repo(&repo)?;
    let store = open_store(&repo)?;
    let mut case_reports = Vec::with_capacity(cases.len());
    let mut recall_sum = 0.0;
    let mut mrr_sum = 0.0;
    let mut ndcg_sum = 0.0;
    let mut context_recall_sum = 0.0;
    let mut test_recall_sum = 0.0;
    let mut abstention_required = 0usize;

    for case in cases {
        let search_results = search(&repo, &store, &case.task, limit)?;
        let context = build_context_pack(&repo, &store, &case.task, limit)?;
        let search_paths = search_results
            .iter()
            .map(|result| result.path.clone())
            .collect::<Vec<_>>();
        let context_paths = context
            .primary_files
            .iter()
            .chain(context.supporting_files.iter())
            .map(|result| result.path.clone())
            .collect::<Vec<_>>();
        let selected_tests = context
            .test_candidates
            .iter()
            .map(|test| test.name.clone())
            .collect::<Vec<_>>();

        let search_ranks = expected_path_ranks(&case.expected_paths, &search_paths);
        let search_hits = search_ranks.iter().filter(|rank| rank.is_some()).count();
        let search_recall = ratio(search_hits, case.expected_paths.len());
        recall_sum += search_recall;
        mrr_sum += reciprocal_rank(&search_ranks);
        ndcg_sum += ndcg(&search_ranks, limit);

        let context_hits = matching_expected_values(&case.expected_paths, &context_paths);
        let context_recall = ratio(context_hits.len(), case.expected_paths.len());
        context_recall_sum += context_recall;

        let test_hits = matching_expected_strings(&case.expected_tests, &selected_tests);
        let test_recall = ratio(test_hits.len(), case.expected_tests.len());
        test_recall_sum += test_recall;

        let mut notes = Vec::new();
        if search_recall == 0.0 {
            notes.push("expected files were not found in top search results".into());
        }
        if context_recall == 0.0 {
            notes.push("expected files were not grounded in context pack".into());
        }
        if !case.expected_tests.is_empty() && test_recall == 0.0 {
            notes.push("expected tests were not selected".into());
        }
        let confidence = if search_recall > 0.0 && context_recall > 0.0 {
            "grounded"
        } else if search_results.is_empty() || context.primary_files.is_empty() {
            abstention_required += 1;
            "abstain"
        } else {
            abstention_required += 1;
            "weak"
        };

        case_reports.push(EvalCaseReport {
            task: case.task,
            expected_paths: case.expected_paths,
            expected_tests: case.expected_tests,
            search_ranks,
            context_hits,
            test_hits,
            top_search_paths: search_paths.into_iter().take(limit).collect(),
            top_context_paths: context_paths.into_iter().take(limit).collect(),
            confidence,
            notes,
        });
    }

    let count = case_reports.len() as f64;
    Ok(EvalReport {
        repo,
        limit,
        case_count: case_reports.len(),
        summary: EvalSummary {
            search_recall_at_k: recall_sum / count,
            search_mrr: mrr_sum / count,
            search_ndcg_at_k: ndcg_sum / count,
            context_recall_at_k: context_recall_sum / count,
            test_recall_at_k: test_recall_sum / count,
            abstention_required,
        },
        cases: case_reports,
    })
}

fn load_eval_cases(
    values: &[String],
    cases_file: Option<&PathBuf>,
) -> anyhow::Result<Vec<EvalCase>> {
    let mut cases = values
        .iter()
        .map(|value| {
            let (task, expected) = value.split_once('=').ok_or_else(|| {
                anyhow::anyhow!("eval case must use TASK=EXPECTED_PATH[,EXPECTED_PATH]: {value}")
            })?;
            let expected_paths = expected
                .split(',')
                .map(str::trim)
                .filter(|path| !path.is_empty())
                .map(ToString::to_string)
                .collect::<Vec<_>>();
            if task.trim().is_empty() || expected_paths.is_empty() {
                anyhow::bail!("eval task and expected paths must be non-empty: {value}");
            }
            Ok(EvalCase {
                task: task.trim().to_string(),
                expected_paths,
                expected_tests: Vec::new(),
            })
        })
        .collect::<anyhow::Result<Vec<_>>>()?;
    if let Some(path) = cases_file {
        let raw = fs::read_to_string(path)?;
        let mut from_file: Vec<EvalCase> = serde_json::from_str(&raw)?;
        cases.append(&mut from_file);
    }
    Ok(cases)
}

fn expected_path_ranks(expected_paths: &[String], actual_paths: &[PathBuf]) -> Vec<Option<usize>> {
    expected_paths
        .iter()
        .map(|expected| {
            let expected = normalize_path_fragment(expected);
            actual_paths
                .iter()
                .position(|path| {
                    normalize_path_fragment(&path.to_string_lossy()).contains(&expected)
                })
                .map(|rank| rank + 1)
        })
        .collect()
}

fn matching_expected_values(expected: &[String], actual: &[PathBuf]) -> Vec<String> {
    expected
        .iter()
        .filter(|expected| {
            let expected = normalize_path_fragment(expected);
            actual
                .iter()
                .any(|path| normalize_path_fragment(&path.to_string_lossy()).contains(&expected))
        })
        .cloned()
        .collect()
}

fn matching_expected_strings(expected: &[String], actual: &[String]) -> Vec<String> {
    expected
        .iter()
        .filter(|expected| {
            let expected = expected.to_ascii_lowercase();
            actual
                .iter()
                .any(|value| value.to_ascii_lowercase().contains(&expected))
        })
        .cloned()
        .collect()
}

fn reciprocal_rank(ranks: &[Option<usize>]) -> f64 {
    ranks
        .iter()
        .flatten()
        .min()
        .map(|rank| 1.0 / *rank as f64)
        .unwrap_or(0.0)
}

fn ndcg(ranks: &[Option<usize>], limit: usize) -> f64 {
    if ranks.is_empty() {
        return 1.0;
    }
    let dcg = ranks
        .iter()
        .flatten()
        .filter(|rank| **rank <= limit)
        .map(|rank| 1.0 / ((*rank as f64) + 1.0).log2())
        .sum::<f64>();
    let ideal = (1..=ranks.len().min(limit))
        .map(|rank| 1.0 / ((rank as f64) + 1.0).log2())
        .sum::<f64>();
    if ideal == 0.0 {
        0.0
    } else {
        dcg / ideal
    }
}

fn ratio(numerator: usize, denominator: usize) -> f64 {
    if denominator == 0 {
        1.0
    } else {
        numerator as f64 / denominator as f64
    }
}

fn print_eval_report(report: &EvalReport) {
    println!("Open Kioku eval for {}", report.repo.display());
    println!(
        "Search recall@{} {:.3}, MRR {:.3}, nDCG@{} {:.3}",
        report.limit,
        report.summary.search_recall_at_k,
        report.summary.search_mrr,
        report.limit,
        report.summary.search_ndcg_at_k
    );
    println!(
        "Context recall@{} {:.3}, test recall@{} {:.3}, weak/abstain {}",
        report.limit,
        report.summary.context_recall_at_k,
        report.limit,
        report.summary.test_recall_at_k,
        report.summary.abstention_required
    );
    for case in &report.cases {
        println!("\n- {} [{}]", case.task, case.confidence);
        println!("  expected paths: {}", case.expected_paths.join(", "));
        println!("  ranks: {:?}", case.search_ranks);
        if !case.test_hits.is_empty() {
            println!("  test hits: {}", case.test_hits.join(", "));
        }
        for note in &case.notes {
            println!("  note: {note}");
        }
    }
}

const DEFAULT_PROOF_TASKS: &[&str] = &[
    "authentication",
    "configuration",
    "tests",
    "security",
    "database",
    "api",
    "mcp",
    "context pack",
    "impact analysis",
    "search code",
    "symbol lookup",
    "release workflow",
    "npm package",
    "policy",
    "validation",
];

fn run_proof(args: ProveArgs) -> anyhow::Result<ProofReport> {
    let repo = absolutize(&args.path)?;
    let limit = args.limit.clamp(1, 100);
    let snapshot = index_repo(&repo)?;
    let store = open_store(&repo)?;
    let files = store.list_files(usize::MAX, 0)?;
    let languages = language_counts(&files);
    let tasks = if args.tasks.is_empty() {
        choose_proof_tasks(&repo, &store, 3)?
    } else {
        args.tasks
            .iter()
            .map(|task| task.trim())
            .filter(|task| !task.is_empty())
            .map(ToString::to_string)
            .collect::<Vec<_>>()
    };
    if tasks.is_empty() {
        anyhow::bail!("no proof tasks were provided or discovered");
    }

    let index_dir = default_index_dir(&repo);
    let search_index = if TantivySearchIndex::exists(&index_dir) {
        Some(TantivySearchIndex::open_or_create(&index_dir)?)
    } else {
        None
    };
    let planner = PlanEngine::new(&store as &dyn OkStore)
        .with_search_index(search_index.as_ref().map(|idx| idx as &dyn SearchIndex));
    let mut task_reports = Vec::with_capacity(tasks.len());
    for task in &tasks {
        let plan = planner.plan(task, limit)?;
        let top_results = search(&repo, &store, task, 5)?;
        task_reports.push(score_proof_task(
            &repo,
            task,
            &plan,
            &top_results,
            args.reveal_paths,
        ));
    }

    let scores = task_reports
        .iter()
        .map(|task| task.score)
        .collect::<Vec<_>>();
    let total = scores.iter().sum::<u32>();
    let tasks_scored = task_reports.len();
    let average_score = if tasks_scored > 0 {
        total as f64 / tasks_scored as f64
    } else {
        0.0
    };
    let pass_rate_70 = if tasks_scored > 0 {
        100.0 * scores.iter().filter(|score| **score >= 70).count() as f64 / tasks_scored as f64
    } else {
        0.0
    };

    Ok(ProofReport {
        repo: if args.reveal_paths {
            repo.display().to_string()
        } else {
            "local repository".into()
        },
        generated_by: "ok prove",
        privacy: ProofPrivacy {
            source_snippets_included: false,
            local_root_included: args.reveal_paths,
            path_mode: if args.reveal_paths {
                "repository_relative"
            } else {
                "redacted_shapes"
            },
        },
        summary: ProofSummary {
            indexed_files: snapshot.manifest.file_count,
            indexed_symbols: snapshot.manifest.symbol_count,
            indexed_chunks: snapshot.manifest.chunk_count,
            tasks_scored,
            average_score: round1(average_score),
            min_score: scores.iter().min().copied().unwrap_or(0),
            max_score: scores.iter().max().copied().unwrap_or(0),
            pass_rate_70: round1(pass_rate_70),
        },
        languages,
        tasks: task_reports,
        reproduce: reproduce_commands(&repo, &tasks, limit, args.reveal_paths),
        notes: vec![
            "The report includes metrics and path shapes only; it does not include source snippets.",
            "Scores measure whether Open Kioku returned grounded planning context, impact, validation, risk, and agent tool calls.",
            "Use --task to evaluate product-specific workflows and --reveal-paths when repository-relative paths are safe to share.",
        ],
    })
}

fn choose_proof_tasks(
    repo: &Path,
    store: &dyn MetadataStore,
    max_tasks: usize,
) -> anyhow::Result<Vec<String>> {
    let mut tasks = Vec::new();
    for candidate in DEFAULT_PROOF_TASKS {
        if !search(repo, store, candidate, 1)?.is_empty() {
            tasks.push((*candidate).to_string());
        }
        if tasks.len() >= max_tasks {
            return Ok(tasks);
        }
    }

    for symbol in store.list_symbols(None, max_tasks, 0)? {
        if !symbol.name.trim().is_empty() {
            tasks.push(symbol.name);
        }
        if tasks.len() >= max_tasks {
            break;
        }
    }
    tasks.sort();
    tasks.dedup();
    Ok(tasks)
}

fn score_proof_task(
    repo: &Path,
    task: &str,
    plan: &open_kioku_core::PlanReport,
    top_results: &[open_kioku_core::SearchResult],
    reveal_paths: bool,
) -> ProofTaskReport {
    let primary_paths = plan
        .primary_context
        .iter()
        .map(|result| result.path.as_path())
        .collect::<Vec<_>>();
    let existing_paths = primary_paths
        .iter()
        .filter(|path| repo.join(path).exists())
        .count();
    let source_context_count = primary_paths
        .iter()
        .filter(|path| is_source_path(path))
        .count();
    let impact_count = plan.impact.direct_impacts.len() + plan.impact.indirect_impacts.len();

    let mut checks = BTreeMap::new();
    checks.insert("primary_context", !plan.primary_context.is_empty());
    checks.insert(
        "paths_exist",
        !primary_paths.is_empty() && existing_paths == primary_paths.len(),
    );
    checks.insert("source_context", source_context_count > 0);
    checks.insert("impact_candidates", impact_count > 0);
    checks.insert("validation_candidates", !plan.validation.is_empty());
    checks.insert("agent_tool_calls", plan.tool_calls.len() >= 3);
    checks.insert("known_risk", plan.risk.level != "unknown");

    let mut score = 0;
    for (name, weight) in [
        ("primary_context", 25),
        ("paths_exist", 15),
        ("source_context", 15),
        ("impact_candidates", 15),
        ("validation_candidates", 15),
        ("agent_tool_calls", 10),
        ("known_risk", 5),
    ] {
        if checks.get(name).copied().unwrap_or(false) {
            score += weight;
        }
    }

    ProofTaskReport {
        task: task.into(),
        score,
        checks,
        primary_context_count: plan.primary_context.len(),
        source_context_count,
        impact_count,
        validation_count: plan.validation.len(),
        tool_call_count: plan.tool_calls.len(),
        risk_level: plan.risk.level.clone(),
        sample_paths: redact_paths(primary_paths, reveal_paths),
        top_search_paths: redact_paths(
            top_results
                .iter()
                .map(|result| result.path.as_path())
                .collect::<Vec<_>>(),
            reveal_paths,
        ),
    }
}

fn language_counts(files: &[open_kioku_core::File]) -> BTreeMap<String, usize> {
    let mut counts = BTreeMap::new();
    for file in files {
        *counts
            .entry(format!("{:?}", file.language).to_ascii_lowercase())
            .or_insert(0) += 1;
    }
    counts
}

fn is_source_path(path: &Path) -> bool {
    !is_doc_path(path) && !is_test_path(path)
}

fn is_doc_path(path: &Path) -> bool {
    matches!(
        path.extension().and_then(|value| value.to_str()),
        Some("md" | "mdx" | "txt" | "rst")
    ) || path
        .components()
        .next()
        .and_then(|component| component.as_os_str().to_str())
        == Some("docs")
}

fn is_test_path(path: &Path) -> bool {
    let value = normalize_path_fragment(&path.to_string_lossy());
    value.contains("/test")
        || value.contains("test/")
        || value.contains("/spec")
        || value.ends_with("_test.go")
        || value.ends_with(".test.ts")
        || value.ends_with(".spec.ts")
}

fn redact_paths(paths: Vec<&Path>, reveal_paths: bool) -> Vec<String> {
    let mut values = paths
        .into_iter()
        .map(|path| proof_path(path, reveal_paths))
        .collect::<Vec<_>>();
    values.sort();
    values.dedup();
    values.truncate(5);
    values
}

fn proof_path(path: &Path, reveal_paths: bool) -> String {
    if reveal_paths {
        return path.display().to_string();
    }
    let ext = path
        .extension()
        .and_then(|value| value.to_str())
        .filter(|value| !value.is_empty())
        .unwrap_or("file");
    if path
        .parent()
        .filter(|parent| !parent.as_os_str().is_empty())
        .is_none()
    {
        return format!("**/*.{ext}");
    }
    let top = path
        .components()
        .next()
        .and_then(|component| component.as_os_str().to_str())
        .filter(|value| !value.is_empty())
        .unwrap_or("repo");
    format!("{top}/**/*.{ext}")
}

fn reproduce_commands(
    repo: &Path,
    tasks: &[String],
    limit: usize,
    reveal_paths: bool,
) -> Vec<String> {
    let repo_arg = if reveal_paths {
        repo.display().to_string()
    } else {
        "/path/to/repo".into()
    };
    let mut command = format!("ok prove {repo_arg} --limit {limit}");
    for task in tasks {
        command.push_str(" --task ");
        command.push_str(&shell_quote(task));
    }
    vec![
        format!("ok init {repo_arg}"),
        format!("ok index {repo_arg}"),
        command,
        format!("ok mcp install cursor --repo {repo_arg}"),
        format!("ok mcp install claude --repo {repo_arg}"),
    ]
}

fn shell_quote(value: &str) -> String {
    if value
        .chars()
        .all(|ch| ch.is_ascii_alphanumeric() || matches!(ch, '-' | '_' | '/' | '.'))
    {
        value.into()
    } else {
        format!("'{}'", value.replace('\'', "'\\''"))
    }
}

fn render_proof_markdown(report: &ProofReport) -> String {
    let mut out = String::new();
    out.push_str("# Open Kioku Proof\n\n");
    out.push_str("Generated by `ok prove` against a real local repository.\n\n");
    out.push_str("This report is designed to be shared: it records metrics and path shapes, not source snippets.\n\n");

    out.push_str("## Summary\n\n");
    out.push_str("| Metric | Value |\n");
    out.push_str("| --- | ---: |\n");
    out.push_str(&format!(
        "| Indexed files | {} |\n",
        report.summary.indexed_files
    ));
    out.push_str(&format!(
        "| Indexed symbols | {} |\n",
        report.summary.indexed_symbols
    ));
    out.push_str(&format!(
        "| Indexed chunks | {} |\n",
        report.summary.indexed_chunks
    ));
    out.push_str(&format!(
        "| Tasks scored | {} |\n",
        report.summary.tasks_scored
    ));
    out.push_str(&format!(
        "| Average proof score | {:.1}/100 |\n",
        report.summary.average_score
    ));
    out.push_str(&format!(
        "| Pass rate at 70+ | {:.1}% |\n",
        report.summary.pass_rate_70
    ));

    out.push_str("\n## Languages\n\n");
    for (language, count) in &report.languages {
        out.push_str(&format!("- `{language}`: {count}\n"));
    }

    out.push_str("\n## Task Scores\n\n");
    out.push_str("| Task | Score | Context | Impact | Validation | Risk | Sample paths |\n");
    out.push_str("| --- | ---: | ---: | ---: | ---: | --- | --- |\n");
    for task in &report.tasks {
        out.push_str(&format!(
            "| {} | {} | {} | {} | {} | {} | {} |\n",
            escape_table_cell(&task.task),
            task.score,
            task.primary_context_count,
            task.impact_count,
            task.validation_count,
            escape_table_cell(&task.risk_level),
            escape_table_cell(&task.sample_paths.join(", "))
        ));
    }

    out.push_str("\n## What Was Checked\n\n");
    out.push_str("- Primary context exists for each task.\n");
    out.push_str("- Returned paths exist in the indexed repository.\n");
    out.push_str("- At least one source file appears in context when available.\n");
    out.push_str(
        "- Impact candidates, validation candidates, risk, and agent tool calls are produced.\n",
    );

    out.push_str("\n## Reproduce\n\n");
    out.push_str("```sh\n");
    for command in &report.reproduce {
        out.push_str(command);
        out.push('\n');
    }
    out.push_str("```\n");

    out.push_str("\n## Privacy\n\n");
    out.push_str(&format!(
        "- Source snippets included: `{}`\n",
        report.privacy.source_snippets_included
    ));
    out.push_str(&format!(
        "- Local root included: `{}`\n",
        report.privacy.local_root_included
    ));
    out.push_str(&format!("- Path mode: `{}`\n", report.privacy.path_mode));
    out
}

fn escape_table_cell(value: &str) -> String {
    value.replace('|', "\\|").replace('\n', " ")
}

fn round1(value: f64) -> f64 {
    (value * 10.0).round() / 10.0
}

fn time_searches(
    iterations: usize,
    mut run: impl FnMut() -> open_kioku_errors::Result<()>,
) -> anyhow::Result<Vec<Duration>> {
    let mut times = Vec::with_capacity(iterations);
    for _ in 0..iterations {
        let started = Instant::now();
        run()?;
        times.push(started.elapsed());
    }
    Ok(times)
}

fn median_duration(mut values: Vec<Duration>) -> Duration {
    values.sort();
    values[values.len() / 2]
}

fn duration_ms(duration: Duration) -> f64 {
    duration.as_secs_f64() * 1000.0
}

fn normalize_path_fragment(value: &str) -> String {
    value.replace('\\', "/").to_ascii_lowercase()
}

fn build_context_pack(
    repo: &Path,
    store: &SqliteStore,
    task: &str,
    limit: usize,
) -> anyhow::Result<open_kioku_core::ContextPack> {
    let search_dir = default_index_dir(repo);
    let builder = ContextPackBuilder::new(store as &dyn OkStore);
    if TantivySearchIndex::exists(&search_dir) {
        let index = TantivySearchIndex::open_or_create(&search_dir)?;
        let primary = index.search(task, limit.max(20))?;
        return Ok(builder.build_from_primary(task, limit, primary)?);
    }
    Ok(builder.build(task, limit)?)
}

fn index_repo(repo: &Path) -> anyhow::Result<open_kioku_ingest::IndexSnapshot> {
    index_repo_with_config(repo, OkConfig::load_from_repo(repo)?)
}

fn index_repo_with_scip_mode(
    repo: &Path,
    with_scip: Option<&str>,
) -> anyhow::Result<open_kioku_ingest::IndexSnapshot> {
    let mut config = OkConfig::load_from_repo(repo)?;
    if let Some(mode) = with_scip {
        config.scip.enabled = mode != "off";
        config.scip.mode = parse_scip_mode(mode)?;
    }
    index_repo_with_config(repo, config)
}

fn index_repo_with_config(
    repo: &Path,
    config: OkConfig,
) -> anyhow::Result<open_kioku_ingest::IndexSnapshot> {
    let reporter = Arc::new(Mutex::new(IndexProgressReporter::new()));
    let _lock = IndexWriteLock::acquire(repo, &reporter)?;
    let index_reporter = Arc::clone(&reporter);
    let snapshot = Indexer::default().index_repo_with_progress(repo, &config, move |progress| {
        report_index_progress(&index_reporter, progress);
    })?;
    report_index_stage(
        &reporter,
        "store",
        format!(
            "writing {} files, {} symbols, {} chunks, {} occurrences, {} analysis facts",
            snapshot.files.len(),
            snapshot.symbols.len(),
            snapshot.chunks.len(),
            snapshot.occurrences.len(),
            snapshot.analysis_facts.len()
        ),
    );
    let store = open_store(repo)?;
    store.replace_index(IndexData {
        manifest: &snapshot.manifest,
        files: &snapshot.files,
        symbols: &snapshot.symbols,
        chunks: &snapshot.chunks,
        tests: &snapshot.tests,
        imports: &snapshot.imports,
        occurrences: &snapshot.occurrences,
    })?;
    report_index_stage(&reporter, "graph", "building dependency graph".to_string());
    let graph = InMemoryGraph::from_index_with_analysis(
        &snapshot.files,
        &snapshot.symbols,
        &snapshot.chunks,
        &snapshot.occurrences,
        &snapshot.imports,
        &snapshot.analysis_facts,
    );
    report_index_stage(
        &reporter,
        "graph",
        format!(
            "writing {} graph nodes and {} graph edges",
            graph.nodes.len(),
            graph.edges.len()
        ),
    );
    store.replace_graph(
        &graph.nodes.values().cloned().collect::<Vec<_>>(),
        &graph.edges,
    )?;
    report_index_stage(
        &reporter,
        "search",
        format!(
            "rebuilding Tantivy index for {} chunks",
            snapshot.chunks.len()
        ),
    );
    rebuild_disk_index(
        default_index_dir(repo),
        &snapshot.chunks,
        &snapshot.files,
        &snapshot.symbols,
    )?;
    report_index_stage(&reporter, "complete", "index ready".to_string());
    Ok(snapshot)
}

fn parse_scip_mode(value: &str) -> anyhow::Result<ScipMode> {
    match value {
        "off" => Ok(ScipMode::Off),
        "consume" => Ok(ScipMode::Consume),
        "auto" => Ok(ScipMode::Auto),
        "required" => Ok(ScipMode::Required),
        other => anyhow::bail!("unsupported SCIP mode: {other}"),
    }
}

struct IndexWriteLock {
    path: PathBuf,
    _file: fs::File,
}

impl IndexWriteLock {
    fn acquire(repo: &Path, reporter: &Arc<Mutex<IndexProgressReporter>>) -> anyhow::Result<Self> {
        let ok_dir = repo.join(".ok");
        fs::create_dir_all(&ok_dir)?;
        let lock_path = ok_dir.join("index.lock");
        report_index_stage(
            reporter,
            "lock",
            "waiting for exclusive index writer lock".to_string(),
        );
        let started_waiting = Instant::now();
        let file = loop {
            match fs::OpenOptions::new()
                .write(true)
                .create_new(true)
                .open(&lock_path)
            {
                Ok(file) => break file,
                Err(err) if err.kind() == std::io::ErrorKind::AlreadyExists => {
                    if started_waiting.elapsed() > Duration::from_secs(30) {
                        anyhow::bail!(
                            "index is locked by another writer or a stale lock at {}; remove it only if no ok index process is running",
                            lock_path.display()
                        );
                    }
                    thread::sleep(Duration::from_millis(250));
                }
                Err(err) => return Err(err.into()),
            }
        };
        report_index_stage(reporter, "lock", "acquired index writer lock".to_string());
        Ok(Self {
            path: lock_path,
            _file: file,
        })
    }
}

impl Drop for IndexWriteLock {
    fn drop(&mut self) {
        let _ = fs::remove_file(&self.path);
    }
}

struct IndexProgressReporter {
    started_at: Instant,
    last_emitted_at: Instant,
    last_phase: &'static str,
}

impl IndexProgressReporter {
    fn new() -> Self {
        let now = Instant::now();
        Self {
            started_at: now,
            last_emitted_at: now,
            last_phase: "",
        }
    }

    fn emit_progress(&mut self, progress: IndexProgress) {
        let now = Instant::now();
        let phase_changed = self.last_phase != progress.phase;
        let completed = progress
            .total_files
            .map(|total| progress.indexed_files == total)
            .unwrap_or(false);
        if !phase_changed
            && !completed
            && now.duration_since(self.last_emitted_at) < Duration::from_secs(2)
        {
            return;
        }
        self.last_phase = progress.phase;
        self.last_emitted_at = now;
        let elapsed = self.started_at.elapsed().as_secs_f64();
        match progress.total_files {
            Some(total) if total > 0 => {
                let percent = (progress.indexed_files as f64 / total as f64) * 100.0;
                eprintln!(
                    "index[{phase}] {indexed}/{total} files ({percent:.1}%), scanned={scanned}, elapsed={elapsed:.1}s",
                    phase = progress.phase,
                    indexed = progress.indexed_files,
                    scanned = progress.scanned_files,
                );
            }
            _ => {
                eprintln!(
                    "index[{phase}] scanned={scanned}, indexed={indexed}, elapsed={elapsed:.1}s",
                    phase = progress.phase,
                    scanned = progress.scanned_files,
                    indexed = progress.indexed_files,
                );
            }
        }
    }

    fn emit_stage(&mut self, phase: &'static str, detail: String) {
        let elapsed = self.started_at.elapsed().as_secs_f64();
        self.last_phase = phase;
        self.last_emitted_at = Instant::now();
        eprintln!("index[{phase}] {detail}, elapsed={elapsed:.1}s");
    }
}

fn report_index_progress(reporter: &Arc<Mutex<IndexProgressReporter>>, progress: IndexProgress) {
    if let Ok(mut reporter) = reporter.lock() {
        reporter.emit_progress(progress);
    }
}

fn report_index_stage(
    reporter: &Arc<Mutex<IndexProgressReporter>>,
    phase: &'static str,
    detail: String,
) {
    if let Ok(mut reporter) = reporter.lock() {
        reporter.emit_stage(phase, detail);
    }
}

fn mcp_install_snippet(client: McpClient, repo: &Path) -> serde_json::Value {
    let args = vec![
        "mcp".to_string(),
        "serve".to_string(),
        "--repo".to_string(),
        repo.display().to_string(),
        "--read-only".to_string(),
    ];
    let command_array: Vec<String> = std::iter::once("ok".to_string())
        .chain(args.iter().cloned())
        .collect();
    match client {
        McpClient::Claude => serde_json::json!({
            "client": "claude",
            "instructions": "Add this entry to Claude Desktop's mcpServers config. To enable the apply_patch tool, add an \"env\" object with \"OPEN_KIOKU_ALLOW_WRITE\": \"true\".",
            "config": {
                "mcpServers": {
                    "open-kioku": {
                        "command": "ok",
                        "args": args
                    }
                }
            }
        }),
        McpClient::Cursor => serde_json::json!({
            "client": "cursor",
            "instructions": "Add this entry to Cursor's MCP config. To enable the apply_patch tool, set the environment variable OPEN_KIOKU_ALLOW_WRITE=true.",
            "config": {
                "open-kioku": {
                    "command": "ok",
                    "args": args
                }
            }
        }),
        McpClient::Codex => serde_json::json!({
            "client": "codex",
            "instructions": "Add this entry to ~/.codex/config.toml or your trusted project .codex/config.toml.",
            "config_text": format!(
                "[mcp_servers.open-kioku]\ncommand = \"ok\"\nargs = [{}]\nenabled = true\n",
                args.iter()
                    .map(|arg| format!("\"{}\"", toml_escape(arg)))
                    .collect::<Vec<_>>()
                    .join(", ")
            ),
            "config": {
                "mcp_servers": {
                    "open-kioku": {
                        "command": "ok",
                        "args": args,
                        "enabled": true
                    }
                }
            }
        }),
        McpClient::Gemini => serde_json::json!({
            "client": "gemini",
            "instructions": "Add this entry to .gemini/settings.json or ~/.gemini/settings.json under mcpServers.",
            "config": {
                "mcpServers": {
                    "open-kioku": {
                        "command": "ok",
                        "args": args,
                        "trust": false
                    }
                }
            }
        }),
        McpClient::Opencode => serde_json::json!({
            "client": "opencode",
            "instructions": "Add this entry to opencode.json or opencode.jsonc.",
            "config": {
                "$schema": "https://opencode.ai/config.json",
                "mcp": {
                    "open-kioku": {
                        "type": "local",
                        "command": command_array,
                        "enabled": true
                    }
                }
            }
        }),
        McpClient::Zed => serde_json::json!({
            "client": "zed",
            "instructions": "Add this entry to Zed settings.json under context_servers.",
            "config": {
                "context_servers": {
                    "open-kioku": {
                        "command": "ok",
                        "args": args,
                        "env": {}
                    }
                }
            }
        }),
    }
}

fn toml_escape(value: &str) -> String {
    value.replace('\\', "\\\\").replace('"', "\\\"")
}

fn absolutize(path: &Path) -> anyhow::Result<PathBuf> {
    let path = if path.is_absolute() {
        path.to_path_buf()
    } else {
        std::env::current_dir()?.join(path)
    };
    if path.exists() {
        Ok(path.canonicalize()?)
    } else {
        Ok(path)
    }
}

fn open_store(repo: impl AsRef<Path>) -> anyhow::Result<SqliteStore> {
    Ok(SqliteStore::open(repo.as_ref().join(".ok/index.sqlite"))?)
}

fn search(
    repo: impl AsRef<Path>,
    store: &dyn MetadataStore,
    query: &str,
    limit: usize,
) -> anyhow::Result<Vec<open_kioku_core::SearchResult>> {
    let index_dir = default_index_dir(repo);
    if TantivySearchIndex::exists(&index_dir) {
        return Ok(TantivySearchIndex::open_or_create(index_dir)?.search(query, limit)?);
    }
    let files = store.list_files(usize::MAX, 0)?;
    let chunks = store.all_chunks()?;
    let symbols = store.list_symbols(None, usize::MAX, 0)?;
    Ok(search_chunks(&chunks, &files, &symbols, query, limit)?)
}

fn resolve_repo(global: &Path, command: PathBuf) -> PathBuf {
    if command == Path::new(".") {
        global.to_path_buf()
    } else {
        command
    }
}

fn normalize_to_repo_relative(repo_root: &Path, path: &Path) -> PathBuf {
    let absolute_path = if path.is_absolute() {
        path.to_path_buf()
    } else {
        std::env::current_dir()
            .map(|cwd| cwd.join(path))
            .unwrap_or_else(|_| path.to_path_buf())
    };

    let absolute_repo = std::fs::canonicalize(repo_root)
        .or_else(|_| absolutize(repo_root))
        .unwrap_or_else(|_| repo_root.to_path_buf());

    let absolute_path_canonical = std::fs::canonicalize(&absolute_path)
        .or_else(|_| absolutize(&absolute_path))
        .unwrap_or(absolute_path);

    if let Ok(rel) = absolute_path_canonical.strip_prefix(&absolute_repo) {
        rel.to_path_buf()
    } else if let Ok(rel) = absolute_path_canonical.strip_prefix(repo_root) {
        rel.to_path_buf()
    } else {
        if path.is_absolute() {
            path.to_path_buf()
        } else {
            let mut components = path.components();
            if let Some(std::path::Component::CurDir) = components.next() {
                components.as_path().to_path_buf()
            } else {
                path.to_path_buf()
            }
        }
    }
}

fn resolve_graph_node(store: &dyn MetadataStore, query: &str) -> anyhow::Result<String> {
    if query.starts_with("file:") || query.starts_with("symbol:") {
        return Ok(query.to_string());
    }
    if let Some(file) = store.get_file_by_path(Path::new(query))? {
        return Ok(format!("file:{}", file.path.display()));
    }
    if let Some(symbol) = store
        .list_symbols(Some(query), 10, 0)?
        .into_iter()
        .find(|symbol| symbol.name == query || symbol.qualified_name.ends_with(query))
    {
        return Ok(format!("symbol:{}", symbol.id.0));
    }
    Ok(query.to_string())
}

fn output<T: serde::Serialize>(json: bool, value: &T, human: impl FnOnce()) -> anyhow::Result<()> {
    if json {
        println!("{}", serde_json::to_string_pretty(value)?);
    } else {
        let text = serde_json::to_string_pretty(value)?;
        if text.len() < 4096 {
            println!("{text}");
        } else {
            human();
        }
    }
    Ok(())
}

fn print_text_or_json(json: bool, text: &str, value: &serde_json::Value) -> anyhow::Result<()> {
    if json {
        println!("{}", serde_json::to_string_pretty(value)?);
    } else {
        println!("{text}");
    }
    Ok(())
}