shepherd-cli 6.6.1

The canonical shepherd command-line interface over the per-project registry, run artifacts, and sprint pipeline.
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#[path = "support/plan.rs"]
mod plan_fixture;
mod support;

use sha2::Digest;
use shepherd_cli::shepherd::run::{LaneStatus, RunStatus, Vocabulary};
use shepherd_cli::shepherd::{RunState, dispatch::Role};
use std::io::Write;
use std::path::{Path, PathBuf};
use std::process::{Command, Output, Stdio};
use std::time::{SystemTime, UNIX_EPOCH};

fn binary() -> &'static str {
    env!("CARGO_BIN_EXE_shepherd")
}

fn fixture(label: &str) -> PathBuf {
    let nonce = SystemTime::now()
        .duration_since(UNIX_EPOCH)
        .expect("clock is after epoch")
        .as_nanos();
    let root = std::env::temp_dir().join(format!(
        "shepherd-wave-b2-run-{label}-{}-{nonce:x}",
        std::process::id()
    ));
    std::fs::create_dir_all(&root).expect("create fixture root");
    let status = Command::new("git")
        .args(["init", "--quiet"])
        .current_dir(&root)
        .status()
        .expect("initialize fixture git repository");
    assert!(status.success(), "git init must succeed");
    // Materialize the same bytes the repository's own .gitattributes
    // guarantees (`* text=auto eol=lf`). Windows git defaults to
    // core.autocrlf=true, so a worktree checkout rewrote LF to CRLF and the
    // plan parser refused a file this fixture had just committed itself.
    let eol = Command::new("git")
        .args(["config", "core.autocrlf", "false"])
        .current_dir(&root)
        .status()
        .expect("pin fixture end-of-line policy");
    assert!(eol.success(), "git config core.autocrlf must succeed");
    root
}

fn invoke(root: &Path, args: &[&str]) -> Output {
    Command::new(binary())
        .args(args)
        .current_dir(root)
        .env("SHEPHERD_HOME", root.join("isolated-home"))
        .env("SHEPHERD_MODEL_QUOTA", "128")
        .output()
        .expect("run shepherd binary")
}

fn invoke_with_stdin(root: &Path, args: &[&str], input: serde_json::Value) -> Output {
    let mut child = Command::new(binary())
        .args(args)
        .current_dir(root)
        .env("SHEPHERD_HOME", root.join("isolated-home"))
        .stdin(Stdio::piped())
        .stdout(Stdio::piped())
        .stderr(Stdio::piped())
        .spawn()
        .expect("spawn shepherd binary");
    child
        .stdin
        .take()
        .expect("command stdin")
        .write_all(&serde_json::to_vec(&input).expect("encode command input"))
        .expect("write command stdin");
    child.wait_with_output().expect("wait for shepherd binary")
}

fn primary(root: &Path) -> PathBuf {
    std::fs::canonicalize(root).expect("canonical fixture root")
}

fn text(bytes: &[u8]) -> String {
    String::from_utf8_lossy(bytes).into_owned()
}

fn cleanup(root: &Path) {
    support::remove_dir_all(root)
}

fn orientation_report(
    root: &Path,
    run: &str,
    agent_id: &str,
    kind: &str,
    evidence_path: &str,
    verdict: Option<serde_json::Value>,
) -> serde_json::Value {
    let evidence = root.join(evidence_path);
    let bytes = std::fs::read(&evidence).expect("orientation evidence");
    let digest: String = sha2::Sha256::digest(bytes)
        .iter()
        .map(|byte| format!("{byte:02x}"))
        .collect();
    let entry = serde_json::json!({"path": evidence_path, "sha256": digest, "line": 1});
    let mut report = serde_json::json!({
        "schema": "shepherd.orientation-report/1",
        "run": run,
        "result_id": agent_id,
        "kind": kind,
        "role": kind,
        "read_scope": [evidence_path],
        "status": "complete",
        "summary": format!("{kind} complete"),
        "assumptions": [{"id": format!("{agent_id}-assumption"), "statement": "bounded"}],
        "claims": [{"id": format!("{agent_id}-claim"), "statement": "observed", "evidence": [entry]}],
        "evidence": [entry],
        "caveats": []
    });
    if let Some(verdict) = verdict {
        report["verdict"] = verdict;
    }
    report
}

fn dispatch_orientation_child(
    root: &Path,
    run: &str,
    agent_id: &str,
    kind: &str,
    result_artifact: &str,
) {
    let pre_path = root.join(format!(".shepherd/runs/{run}/orientation-pre.json"));
    let started_at = if kind == "critic" && pre_path.exists() {
        let pre: serde_json::Value =
            serde_json::from_slice(&std::fs::read(pre_path).expect("orientation pre for Critic"))
                .expect("orientation pre JSON");
        pre["created_at"].as_i64().expect("pre created_at") + 1
    } else {
        1
    };
    let role = Role::from_carrier(&format!("shepherd:{kind}")).expect("orientation role");
    plan_fixture::orientation_record(root, run, role, agent_id, result_artifact, started_at);
}

#[test]
fn init_scaffolds_the_layout_v5_run_at_the_primary_root_and_refuses_a_second_init() {
    let root = fixture("init");
    let first = invoke(
        &root,
        &[
            "run",
            "init",
            "v900-dev0",
            "--kind",
            "sprint",
            "--branch",
            "v9.0.0-dev.0",
            "--base",
            "main",
        ],
    );
    assert_eq!(
        first.status.code(),
        Some(0),
        "stderr={}",
        text(&first.stderr)
    );
    assert_eq!(
        text(&first.stdout),
        format!(
            "{}\n",
            primary(&root)
                .join(".shepherd/runs/v900-dev0/run.json")
                .display()
        )
    );
    let directory = "lanes";
    assert!(
        root.join(".shepherd/runs/v900-dev0")
            .join(directory)
            .is_dir(),
        "{directory} is part of the canonical layout-v5 run shape"
    );

    let second = invoke(&root, &["run", "init", "v900-dev0"]);
    assert_eq!(second.status.code(), Some(5));
    assert_eq!(
        text(&second.stderr),
        "ERROR: run already exists: v900-dev0\n"
    );
    cleanup(&root);
}

#[test]
fn invalid_ids_missing_runs_and_schema_ahead_documents_have_stable_exit_codes_without_writes() {
    let root = fixture("fail-closed");
    let invalid = invoke(&root, &["run", "init", "../escape"]);
    assert_eq!(invalid.status.code(), Some(2));
    assert!(!root.join(".shepherd/runs").exists());

    let absent = invoke(&root, &["run", "show", "v900-dev0"]);
    assert_eq!(absent.status.code(), Some(5));
    assert_eq!(
        text(&absent.stderr),
        format!(
            "ERROR: no such run: v900-dev0 (expected {})\n",
            primary(&root)
                .join(".shepherd/runs/v900-dev0/run.json")
                .display()
        )
    );

    let run = root.join(".shepherd/runs/v900-dev0");
    std::fs::create_dir_all(&run).expect("create run fixture");
    let future =
        b"{\"schema_version\":2,\"run\":\"v900-dev0\",\"status\":\"paused-by-future-host\"}\n";
    std::fs::write(run.join("run.json"), future).expect("write future document");
    let claim = invoke(&root, &["run", "claim", "v900-dev0"]);
    assert_eq!(claim.status.code(), Some(2));
    assert_eq!(
        std::fs::read(run.join("run.json")).expect("read unchanged future document"),
        future
    );
    cleanup(&root);
}

#[test]
fn lifecycle_lane_wave_layout_and_read_only_routes_cover_the_native_surface() {
    let root = fixture("surface");
    let init = invoke(&root, &["run", "init", "v901-dev0"]);
    assert_eq!(init.status.code(), Some(0), "stderr={}", text(&init.stderr));

    for args in [
        &[
            "run",
            "set",
            "v901-dev0",
            "--seed",
            "runs/v901-dev0/seed.md",
            "--plan",
            "runs/v901-dev0/plan.md",
        ][..],
        &[
            "run",
            "lane",
            "add",
            "v901-dev0",
            "l1-engine",
            "--branch",
            "lane/l1",
        ][..],
        &[
            "run",
            "lane",
            "set",
            "v901-dev0",
            "l1-engine",
            "--state",
            "in-progress",
        ][..],
        &[
            "run",
            "wave",
            "accept",
            "v901-dev0",
            "l1-engine",
            "--commit",
            "abc123",
        ][..],
    ] {
        let result = invoke(&root, args);
        assert_eq!(
            result.status.code(),
            Some(0),
            "args={args:?} stderr={}",
            text(&result.stderr)
        );
    }
    let pending = invoke(&root, &["run", "wave", "pending", "v901-dev0"]);
    assert_eq!(pending.status.code(), Some(6));
    assert_eq!(text(&pending.stdout), "l1-engine\tabc123\n");
    let merged = invoke(&root, &["run", "wave", "merged", "v901-dev0", "l1-engine"]);
    assert_eq!(
        merged.status.code(),
        Some(0),
        "stderr={}",
        text(&merged.stderr)
    );
    let clear = invoke(&root, &["run", "wave", "pending", "v901-dev0", "--json"]);
    assert_eq!(clear.status.code(), Some(0));
    assert!(text(&clear.stdout).contains("\"ok\":true"));

    std::fs::write(
        root.join(".shepherd/runs/v901-dev0/lanes/l1-engine/plan.md"),
        "### W1-L1-S1: native command\n",
    )
    .expect("lane plan");
    std::fs::write(
        root.join(".shepherd/runs/v901-dev0/auditor-verdicts.txt"),
        "L1 w1-s1 PASS completed\n",
    )
    .expect("ledger");
    let verified = invoke(&root, &["run", "wave", "verify", "v901-dev0"]);
    assert_eq!(
        verified.status.code(),
        Some(0),
        "stderr={}",
        text(&verified.stderr)
    );
    assert_eq!(
        text(&verified.stdout),
        "W1-L1-S1\tPASS\tL1 w1-s1 PASS completed\n"
    );

    let show = invoke(&root, &["run", "show", "v901-dev0", "--json"]);
    assert_eq!(show.status.code(), Some(0));
    assert!(text(&show.stdout).contains("\"l1-engine\""));
    let listed = invoke(&root, &["run", "list", "--json"]);
    assert_eq!(text(&listed.stdout), "[\"v901-dev0\"]\n");
    let ledger = invoke(&root, &["run", "ledger", "path", "v901-dev0"]);
    assert_eq!(ledger.status.code(), Some(0));
    assert!(text(&ledger.stdout).ends_with(".shepherd/runs/v901-dev0/auditor-verdicts.txt\n"));
    let checked = invoke(&root, &["run", "ledger", "check", "v901-dev0", "--json"]);
    assert_eq!(
        checked.status.code(),
        Some(0),
        "stderr={}",
        text(&checked.stderr)
    );
    let layout = invoke(&root, &["run", "layout", "v901-dev0", "--json"]);
    assert_eq!(layout.status.code(), Some(0));
    assert!(text(&layout.stdout).contains("\"ok\": true"));
    cleanup(&root);
}

#[cfg(unix)]
#[test]
fn symlinked_run_state_is_refused_without_following_the_link() {
    let root = fixture("symlink");
    let outside = fixture("outside");
    std::fs::create_dir_all(root.join(".shepherd/runs/v902-dev0")).expect("run directory");
    std::fs::write(outside.join("state.json"), b"{\"run\":\"v902-dev0\"}\n")
        .expect("outside state");
    std::os::unix::fs::symlink(
        outside.join("state.json"),
        root.join(".shepherd/runs/v902-dev0/run.json"),
    )
    .expect("symlink state");
    let show = invoke(&root, &["run", "show", "v902-dev0"]);
    assert_ne!(show.status.code(), Some(0));
    assert!(text(&show.stderr).contains("symlink"));
    assert_eq!(
        std::fs::read(outside.join("state.json")).expect("outside unchanged"),
        b"{\"run\":\"v902-dev0\"}\n"
    );
    cleanup(&outside);
    cleanup(&root);
}

#[test]
fn rename_canonicalize_and_migrate_preserve_the_run_lifecycle_contract() {
    let root = fixture("migration");
    let init = invoke(&root, &["run", "init", "v903-dev0"]);
    assert_eq!(init.status.code(), Some(0));
    let renamed = invoke(&root, &["run", "rename", "v903-dev0", "v904-dev0-codex-01"]);
    assert_eq!(
        renamed.status.code(),
        Some(0),
        "stderr={}",
        text(&renamed.stderr)
    );
    let canonicalized = invoke(&root, &["run", "canonicalize", "v904-dev0-codex-01"]);
    assert_eq!(
        canonicalized.status.code(),
        Some(0),
        "stderr={}",
        text(&canonicalized.stderr)
    );
    assert!(root.join(".shepherd/runs/v904-dev0/run.json").is_file());

    let legacy = root.join(".shepherd/runs/v905-dev0");
    std::fs::create_dir_all(&legacy).expect("legacy directory");
    std::fs::write(
        legacy.join("run.json"),
        b"{\"run_id\":\"v905-dev0\",\"lanes\":{\"l1-engine\":{\"state\":\"pending\"}},\"updated_at\":\"42\"}\n",
    )
    .expect("legacy run document");
    let migrated = invoke(&root, &["run", "migrate", "v905-dev0"]);
    assert_eq!(
        migrated.status.code(),
        Some(0),
        "stderr={}",
        text(&migrated.stderr)
    );
    let state: serde_json::Value =
        serde_json::from_slice(&std::fs::read(legacy.join("run.json")).expect("migrated state"))
            .expect("canonical JSON");
    assert_eq!(state["run"], "v905-dev0");
    assert_eq!(state["lanes"][0]["id"], "l1-engine");
    cleanup(&root);
}

fn file_digest(path: &Path) -> String {
    sha2::Sha256::digest(std::fs::read(path).expect("digest input"))
        .iter()
        .map(|byte| format!("{byte:02x}"))
        .collect()
}

#[test]
fn orientation_is_native_two_phase_and_planned_transition_cannot_bypass_final_post() {
    let root = fixture("orientation");
    let run = "v907-dev0";
    let init = invoke(&root, &["run", "init", run]);
    assert_eq!(init.status.code(), Some(0), "stderr={}", text(&init.stderr));
    std::fs::write(
        root.join(".shepherd/project.json"),
        br#"{"id":"018f47ce-72d7-7f64-9eb1-2f651d521c2a","scaffolded_at":1000}"#,
    )
    .expect("project identity");
    let run_dir = root.join(".shepherd/runs").join(run);
    plan_fixture::seed(&root, run);
    let seed_path = format!(".shepherd/runs/{run}/seed.md");
    let seed_bytes = std::fs::read(run_dir.join("seed.md")).expect("typed seed");
    std::fs::write(root.join("seed.md"), b"verified seed\n").expect("project seed");
    let seed_hash = file_digest(&run_dir.join("seed.md"));
    let phase0 = format!(
        "# Orientation\n\n## Run and seed\n- run: {run}\n- verified seed path: {seed_path}\n- seed hash: {seed_hash}\n- planted observation: status=planted\n\n## Auditor briefs\n### auditor-1\n- question: reproduce the seeded claim\n- exact read scope: seed.md\n- output path: reports/auditor-1.json\n- budget: bounded\n- result hash: native\n\n## Discovery briefs\n### discovery-1\n- question: resolve the external unknown\n- exact read scope: seed.md\n- output path: reports/discovery-1.json\n- budget: bounded\n- result hash: native\n\n## Assumptions and decisions\n- A-1: unsupported claims remain caveats.\n\n## Coverage map\n- seed deliverable -> orientation evidence.\n\n## Self-review\n- PASS: native pre gate is pending until child results are stopped.\n\n## Critic loop\n- pre-critic: Critic is not dispatched before native pre acceptance.\n- native post gate: pending.\n"
    );
    std::fs::write(run_dir.join("phase0.md"), &phase0).expect("phase0");

    let direct_planned = invoke(&root, &["run", "transition", run, "--to", "planned"]);
    assert_ne!(
        direct_planned.status.code(),
        Some(0),
        "planned bypassed orientation"
    );
    let post_before_pre = invoke(&root, &["run", "orientation", "post", run]);
    assert_ne!(
        post_before_pre.status.code(),
        Some(0),
        "post existed before pre"
    );
    std::fs::write(run_dir.join("seed.md"), b"stale project seed\n").expect("mutate seed");
    let stale_seed_pre = invoke(&root, &["run", "orientation", "pre", run]);
    assert_ne!(
        stale_seed_pre.status.code(),
        Some(0),
        "stale verified seed bypassed native pre"
    );
    std::fs::write(run_dir.join("seed.md"), seed_bytes).expect("restore typed seed");

    std::fs::create_dir_all(run_dir.join("reports")).expect("reports");
    let auditor_path = run_dir.join("reports/auditor-1.json");
    let discovery_path = run_dir.join("reports/discovery-1.json");
    std::fs::write(
        &auditor_path,
        serde_json::to_vec_pretty(&orientation_report(
            &root,
            run,
            "auditor-1",
            "auditor",
            "seed.md",
            None,
        ))
        .expect("auditor JSON"),
    )
    .expect("auditor report");
    std::fs::write(
        &discovery_path,
        serde_json::to_vec_pretty(&orientation_report(
            &root,
            run,
            "discovery-1",
            "discovery",
            "seed.md",
            None,
        ))
        .expect("discovery JSON"),
    )
    .expect("discovery report");
    dispatch_orientation_child(&root, run, "engineer-1", "engineer", "phase0.md");
    dispatch_orientation_child(&root, run, "auditor-1", "auditor", "reports/auditor-1.json");
    dispatch_orientation_child(
        &root,
        run,
        "discovery-1",
        "discovery",
        "reports/discovery-1.json",
    );
    dispatch_orientation_child(
        &root,
        run,
        "critic-before-pre",
        "critic",
        "reports/critic-before-pre.json",
    );
    let critic_before_pre = invoke(&root, &["run", "orientation", "pre", run]);
    assert!(!critic_before_pre.status.success());
    let critic_error = text(&critic_before_pre.stderr);
    assert!(
        critic_error.to_ascii_lowercase().contains("critic"),
        "precreated Critic rejection must name the invalid phase ordering: {critic_error}"
    );
    std::fs::remove_file(run_dir.join("dispatch/critic-before-pre.json"))
        .expect("remove precreated Critic fixture");

    let valid_engineer_dispatch = run_dir.join("dispatch/engineer-1.json");
    let valid_engineer_bytes =
        std::fs::read(&valid_engineer_dispatch).expect("valid Engineer dispatch");
    let mut forged_engineer: serde_json::Value =
        serde_json::from_slice(&valid_engineer_bytes).expect("Engineer dispatch JSON");
    forged_engineer["write_scope"] = serde_json::json!(["plan.md"]);
    forged_engineer["result_artifact"] = serde_json::json!("plan.md");
    std::fs::write(
        &valid_engineer_dispatch,
        serde_json::to_vec(&forged_engineer).expect("forged Engineer dispatch"),
    )
    .expect("write forged Engineer dispatch");
    let wrong_engineer = invoke(&root, &["run", "orientation", "pre", run]);
    assert_ne!(wrong_engineer.status.code(), Some(0));
    std::fs::write(&valid_engineer_dispatch, valid_engineer_bytes)
        .expect("restore Engineer dispatch");

    #[cfg(unix)]
    {
        let outside_phase0 = root.join("outside-phase0.md");
        std::fs::write(&outside_phase0, phase0.as_bytes()).expect("outside phase0");
        std::fs::remove_file(run_dir.join("phase0.md")).expect("remove phase0");
        std::os::unix::fs::symlink(&outside_phase0, run_dir.join("phase0.md"))
            .expect("symlink phase0");
        let linked_phase0 = invoke(&root, &["run", "orientation", "pre", run]);
        assert_ne!(linked_phase0.status.code(), Some(0));
        std::fs::remove_file(run_dir.join("phase0.md")).expect("remove phase0 symlink");
        std::fs::write(run_dir.join("phase0.md"), phase0.as_bytes()).expect("restore phase0");
    }

    let pre = invoke(&root, &["run", "orientation", "pre", run, "--json"]);
    assert_eq!(pre.status.code(), Some(0), "stderr={}", text(&pre.stderr));
    let pre_value: serde_json::Value = serde_json::from_slice(&pre.stdout).expect("pre JSON");
    assert_eq!(pre_value["accepted"], true);
    let pre_path = run_dir.join("orientation-pre.json");
    let pre_hash = file_digest(&pre_path);
    let state_after_pre: serde_json::Value = serde_json::from_slice(
        &std::fs::read(run_dir.join("run.json")).expect("state after native pre"),
    )
    .expect("state after native pre is JSON");
    assert_eq!(state_after_pre["orientation_epoch"], 1);
    let manifest_doc: serde_json::Value = serde_json::from_slice(
        &std::fs::read(run_dir.join("orientation-manifest.json")).expect("manifest"),
    )
    .expect("manifest JSON");
    let pre_doc: serde_json::Value =
        serde_json::from_slice(&std::fs::read(&pre_path).expect("pre")).expect("pre JSON");
    assert_eq!(manifest_doc["orientation_epoch"], 1);
    assert_eq!(pre_doc["orientation_epoch"], 1);
    let replay_pre = invoke(&root, &["run", "orientation", "pre", run, "--json"]);
    assert_eq!(
        replay_pre.status.code(),
        Some(0),
        "committed pre replay failed: {}",
        text(&replay_pre.stderr)
    );
    let replay_value: serde_json::Value =
        serde_json::from_slice(&replay_pre.stdout).expect("replay pre JSON");
    assert_eq!(
        replay_value["manifest_sha256"],
        pre_value["manifest_sha256"]
    );
    assert_eq!(replay_value["pre_sha256"], pre_value["pre_sha256"]);

    let mut crashed_state = state_after_pre.clone();
    crashed_state["orientation_epoch"] = serde_json::json!(0);
    std::fs::write(
        run_dir.join("run.json"),
        serde_json::to_vec_pretty(&crashed_state).expect("crashed state JSON"),
    )
    .expect("simulate crash before run-state publication");
    let recovered = invoke(&root, &["run", "orientation", "pre", run, "--json"]);
    assert_eq!(
        recovered.status.code(),
        Some(0),
        "registry-ahead pre recovery failed: {}",
        text(&recovered.stderr)
    );
    let replay_state: serde_json::Value = serde_json::from_slice(
        &std::fs::read(run_dir.join("run.json")).expect("state after recovery"),
    )
    .expect("recovered state JSON");
    assert_eq!(replay_state["orientation_epoch"], 1);
    assert!(run_dir.join("orientation-manifest.json").is_file());
    assert!(!run_dir.join("orientation-post.json").exists());

    plan_fixture::materialize(&root, run, &["lane-a"], 3);
    let critic_path = run_dir.join("reports/critic-1.json");
    let critic = orientation_report(
        &root,
        run,
        "critic-1",
        "critic",
        "seed.md",
        Some(serde_json::json!({
            "decision": "GREEN",
            "findings": [],
            "corrections": [],
            "blockers": [],
            "citations": [
                {"source_id": "auditor-1", "path": "reports/auditor-1.json", "sha256": file_digest(&auditor_path), "line": 1},
                {"claim_id": "auditor-1-claim"}
            ]
        })),
    );
    let mut critic = critic;
    plan_fixture::add_planning_evidence(&root, run, &mut critic);
    critic["orientation_pre_sha256"] = serde_json::Value::String(pre_hash.clone());
    std::fs::write(
        &critic_path,
        serde_json::to_vec_pretty(&critic).expect("critic JSON"),
    )
    .expect("critic report");
    dispatch_orientation_child(&root, run, "critic-1", "critic", "reports/critic-1.json");
    let mut circular = critic.clone();
    circular["verdict"]["citations"]
        .as_array_mut()
        .expect("Critic citations")
        .push(serde_json::json!({"claim_id": "critic-1-claim"}));
    std::fs::write(
        &critic_path,
        serde_json::to_vec_pretty(&circular).expect("circular critic JSON"),
    )
    .expect("circular critic report");
    let circular_post = invoke(&root, &["run", "orientation", "post", run]);
    assert_ne!(
        circular_post.status.code(),
        Some(0),
        "Critic accepted a citation to its own claim"
    );
    std::fs::write(
        &critic_path,
        serde_json::to_vec_pretty(&critic).expect("restored critic JSON"),
    )
    .expect("restore critic report");

    let post = invoke(&root, &["run", "orientation", "post", run, "--json"]);
    assert_eq!(post.status.code(), Some(0), "stderr={}", text(&post.stderr));
    let post_value: serde_json::Value = serde_json::from_slice(&post.stdout).expect("post JSON");
    assert_eq!(post_value["accepted"], true);
    assert_eq!(post_value["pre_sha256"], pre_hash);
    let post_doc: serde_json::Value = serde_json::from_slice(
        &std::fs::read(run_dir.join("orientation-post.json")).expect("post"),
    )
    .expect("post JSON");
    assert_eq!(post_doc["orientation_epoch"], 1);
    let state_after_post: serde_json::Value =
        serde_json::from_slice(&std::fs::read(run_dir.join("run.json")).expect("state after post"))
            .expect("state after post is JSON");
    assert_eq!(state_after_post["orientation_epoch"], 1);

    let plan_path = run_dir.join("plan.md");
    let verified_plan = std::fs::read(&plan_path).expect("reviewed plan");
    std::fs::remove_file(&plan_path).expect("temporarily missing fixture plan");
    let no_plan = invoke(&root, &["run", "transition", run, "--to", "planned"]);
    assert!(
        !no_plan.status.success(),
        "orientation alone accepted execution-ready state"
    );
    assert_eq!(
        RunState::load(&run_dir.join("run.json"))
            .expect("unchanged planted state")
            .status,
        Vocabulary::Known(RunStatus::Planted)
    );
    std::fs::write(&plan_path, verified_plan).expect("restore reviewed plan");

    // Planned is a native recomputation boundary, not a caller-supplied
    // status shortcut. A forged post is replaced from the current dispatch
    // ledger before the state transition is allowed.
    std::fs::write(run_dir.join("orientation-post.json"), b"{}\n").expect("forge post");
    let recomputed = invoke(&root, &["run", "transition", run, "--to", "planned"]);
    assert_eq!(
        recomputed.status.code(),
        Some(0),
        "stderr={}",
        text(&recomputed.stderr)
    );
    let recomputed_post: serde_json::Value = serde_json::from_slice(
        &std::fs::read(run_dir.join("orientation-post.json")).expect("recomputed post"),
    )
    .expect("recomputed post JSON");
    assert_eq!(recomputed_post["accepted"], true);
    let planned_state: serde_json::Value =
        serde_json::from_slice(&std::fs::read(run_dir.join("run.json")).expect("planned state"))
            .expect("planned state JSON");
    assert_eq!(planned_state["status"], "planned");
    assert_eq!(planned_state["orientation_epoch"], 1);
    assert_eq!(
        invoke(&root, &["run", "transition", run, "--to", "planted"])
            .status
            .code(),
        Some(0)
    );

    std::fs::write(phase0_path(&run_dir), b"# Orientation\nchanged\n").expect("mutate phase0");
    let stale = invoke(&root, &["run", "transition", run, "--to", "planned"]);
    assert_ne!(
        stale.status.code(),
        Some(0),
        "stale post permitted planned transition"
    );
    assert!(text(&invoke(&root, &["run", "show", run, "--json"]).stdout).contains("planted"));
    std::fs::write(run_dir.join("phase0.md"), phase0).expect("restore phase0");
    let planned = invoke(&root, &["run", "transition", run, "--to", "planned"]);
    assert_eq!(
        planned.status.code(),
        Some(0),
        "stderr={}",
        text(&planned.stderr)
    );

    let planned_bytes = std::fs::read(run_dir.join("run.json")).expect("planned state bytes");
    let verified = invoke(&root, &["plan", "verify", "--run", run, "--json"]);
    assert!(
        verified.status.success(),
        "planned verification: {}",
        text(&verified.stderr)
    );
    for path in [
        run_dir.join("plan.md"),
        run_dir.join("seed.md"),
        run_dir.join("mesh.md"),
        run_dir.join("phase0.md"),
        run_dir.join("graph/topology.json"),
        run_dir.join("lanes/lane-a/plan.md"),
        run_dir.join("plan-probes.json"),
        run_dir.join("orientation-post.json"),
        root.join("src/plan-fixture-0.rs"),
    ] {
        let original = std::fs::read(&path).expect("bound artifact");
        let mut changed = original.clone();
        changed.extend_from_slice(b"\nchanged after native planning\n");
        std::fs::write(&path, changed).expect("change bound artifact");
        for args in [
            vec!["sprint", "open", "--run", run],
            vec!["run", "transition", run, "--to", "executing"],
        ] {
            let refused = invoke(&root, &args);
            assert!(
                !refused.status.success(),
                "{} changed but execution opened",
                path.display()
            );
            assert_eq!(
                std::fs::read(run_dir.join("run.json")).expect("unchanged state"),
                planned_bytes
            );
        }
        std::fs::write(path, original).expect("restore exact bound bytes");
    }

    let probes_path = run_dir.join("plan-probes.json");
    let probes = std::fs::read(&probes_path).expect("canonical probes");
    std::fs::remove_file(&probes_path).expect("remove canonical probes fixture");
    std::fs::write(
        run_dir.join("plan-check.json"),
        b"{\"ok\":true,\"accepted\":true}\n",
    )
    .expect("caller-forged successful report");
    let no_probes = invoke(&root, &["sprint", "open", "--run", run]);
    assert!(
        !no_probes.status.success(),
        "a caller-authored report replaced canonical probes"
    );
    assert_eq!(
        std::fs::read(run_dir.join("run.json")).expect("unchanged state"),
        planned_bytes
    );
    std::fs::write(&probes_path, probes).expect("restore canonical probes");

    let mut forged_state: serde_json::Value =
        serde_json::from_slice(&planned_bytes).expect("state JSON");
    forged_state["plan"] = serde_json::json!("");
    std::fs::write(
        run_dir.join("run.json"),
        serde_json::to_vec(&forged_state).expect("forged state"),
    )
    .expect("fixture removes plan pointer");
    let no_pointer = invoke(&root, &["sprint", "open", "--run", run]);
    assert!(
        !no_pointer.status.success(),
        "planned state without exact plan pointer was accepted"
    );
    std::fs::write(run_dir.join("run.json"), planned_bytes).expect("restore exact native state");

    let planning_bind = invoke_with_stdin(
        &root,
        &["dispatch", "bind-root"],
        serde_json::json!({
            "schema": "shepherd.dispatch-request/1",
            "run": run,
            "harness": "codex",
            "session_id": "root-session",
            "role_carrier": "shepherd:shepherd",
            "mode": "planning",
            "lease_ms": 60000
        }),
    );
    assert_eq!(
        planning_bind.status.code(),
        Some(0),
        "planning bind stderr={}",
        text(&planning_bind.stderr)
    );
    let opened = invoke(&root, &["sprint", "open", "--run", run]);
    assert_eq!(
        opened.status.code(),
        Some(0),
        "verified planned sprint open stderr={}",
        text(&opened.stderr)
    );
    let execution_bind = invoke_with_stdin(
        &root,
        &["dispatch", "bind-root"],
        serde_json::json!({
            "schema": "shepherd.dispatch-request/1",
            "run": run,
            "harness": "codex",
            "session_id": "root-session",
            "role_carrier": "shepherd:shepherd",
            "mode": "execution",
            "lease_ms": 60000
        }),
    );
    assert_eq!(
        execution_bind.status.code(),
        Some(0),
        "execution rebind stderr={}",
        text(&execution_bind.stderr)
    );
    let execution_binding: serde_json::Value =
        serde_json::from_slice(&execution_bind.stdout).expect("execution binding JSON");
    assert_eq!(execution_binding["mode"], "execution");
    let resolved = invoke_with_stdin(
        &root,
        &["dispatch", "resolve"],
        serde_json::json!({
            "schema": "shepherd.dispatch-request/1",
            "run": run,
            "harness": "codex",
            "session_id": "root-session"
        }),
    );
    assert_eq!(
        resolved.status.code(),
        Some(0),
        "execution resolve stderr={}",
        text(&resolved.stderr)
    );
    let resolution: serde_json::Value =
        serde_json::from_slice(&resolved.stdout).expect("execution resolution JSON");
    assert_eq!(resolution["run"], run);
    assert_eq!(resolution["mode"], "execution");
    cleanup(&root);
}

fn phase0_path(run_dir: &Path) -> PathBuf {
    run_dir.join("phase0.md")
}

#[test]
fn native_run_init_mints_unforgeable_incarnation_and_rejects_recreated_run_ids() {
    let root = fixture("native-incarnation");
    let run = "v910-dev0";
    let init = invoke(&root, &["run", "init", run]);
    assert_eq!(init.status.code(), Some(0), "stderr={}", text(&init.stderr));

    let state_path = root.join(".shepherd/runs").join(run).join("run.json");
    let state: serde_json::Value =
        serde_json::from_slice(&std::fs::read(&state_path).expect("native run state"))
            .expect("native run state JSON");
    let incarnation = state["run_incarnation"]
        .as_str()
        .expect("native run incarnation")
        .to_owned();
    assert!(!incarnation.is_empty());
    assert_eq!(state["orientation_epoch"], 0);
    assert!(
        root.join(".shepherd/native-orientation-registry.json")
            .is_file()
    );

    std::fs::remove_dir_all(root.join(".shepherd/runs").join(run)).expect("remove old run");
    let recreated = invoke(&root, &["run", "init", run]);
    assert_ne!(recreated.status.code(), Some(0), "run id was reusable");
    assert!(text(&recreated.stderr).contains("incarnation"));
    cleanup(&root);
}

#[test]
fn planned_transition_rejects_identity_mutation_in_the_same_command() {
    let root = fixture("planned-identity-mutation");
    let run = "v911-dev0";
    let init = invoke(&root, &["run", "init", run]);
    assert_eq!(init.status.code(), Some(0), "stderr={}", text(&init.stderr));
    let before = std::fs::read(root.join(".shepherd/runs").join(run).join("run.json"))
        .expect("state before mutation");
    let result = invoke(
        &root,
        &[
            "run",
            "set",
            run,
            "--status",
            "planned",
            "--seed",
            "attacker.md",
        ],
    );
    assert_ne!(
        result.status.code(),
        Some(0),
        "identity mutation was accepted"
    );
    assert_eq!(
        std::fs::read(root.join(".shepherd/runs").join(run).join("run.json"))
            .expect("state after mutation"),
        before,
        "rejected transition must not mutate native state"
    );
    cleanup(&root);
}

#[test]
fn direct_executing_status_cannot_bypass_native_planning_readiness() {
    let root = fixture("executing-gate");
    let init = invoke(&root, &["init", "--confirm"]);
    assert!(init.status.success(), "{}", text(&init.stderr));
    let run = "v908";
    let initialized = invoke(&root, &["run", "init", run]);
    assert!(
        initialized.status.success(),
        "{}",
        text(&initialized.stderr)
    );
    let state_path = root.join(format!(".shepherd/runs/{run}/run.json"));
    let before = std::fs::read(&state_path).expect("initial state");
    for args in [
        vec!["run", "transition", run, "--to", "executing"],
        vec!["sprint", "open", "--run", run],
    ] {
        let denied = invoke(&root, &args);
        assert!(
            !denied.status.success(),
            "unverified execution was accepted: {}",
            text(&denied.stdout)
        );
        assert_eq!(
            std::fs::read(&state_path).expect("unmodified state"),
            before
        );
    }
    cleanup(&root);
}

#[test]
fn native_plan_fixture_opens_only_after_plan_and_orientation_acceptance() {
    for lanes in [
        vec!["lane-a"],
        vec!["lane-a", "lane-b"],
        vec!["lane-a", "lane-b", "lane-c", "lane-d", "lane-e", "lane-f"],
    ] {
        let root = fixture("native-planning-fixture");
        let run = "v909-dev0";
        let baseline = plan_fixture::open_execution(&root, run, &lanes, 3);
        let state_path = root.join(format!(".shepherd/runs/{run}/run.json"));
        let state = RunState::load(&state_path).expect("native executing state");
        assert_eq!(state.status, Vocabulary::Known(RunStatus::Executing));
        assert_eq!(
            state.lanes.len(),
            lanes.len(),
            "execution must bind every verified lane"
        );
        for (expected, lane) in lanes.iter().zip(&state.lanes) {
            assert_eq!(lane.id, *expected);
            assert_eq!(lane.plan, format!("lanes/{expected}/plan.md"));
            assert_eq!(lane.state, Vocabulary::Known(LaneStatus::Pending));
            assert!(lane.accepted_commit.is_none() && !lane.merged);
        }
        let close = invoke(&root, &["sprint", "close", "--run", run]);
        assert!(
            !close.status.success(),
            "pending verified lanes permitted vacuous close"
        );
        let post: serde_json::Value = serde_json::from_slice(
            &std::fs::read(root.join(format!(".shepherd/runs/{run}/orientation-post.json")))
                .expect("native planned checkpoint"),
        )
        .expect("checkpoint JSON");
        assert_eq!(post["planning"]["schema"], "shepherd.plan-readiness/1");
        assert_eq!(post["planning"]["baseline"], baseline);
        assert_eq!(post["planning"]["probe_count"], lanes.len());
        cleanup(&root);
    }
}

#[test]
fn planned_requires_critic_hashes_for_every_canonical_artifact() {
    let root = fixture("critic-plan-hashes");
    let run = "v914";
    plan_fixture::prepare_execution(&root, run, &["lane-a"], 3);
    assert!(
        invoke(&root, &["run", "transition", run, "--to", "planted"])
            .status
            .success()
    );
    let directory = root.join(format!(".shepherd/runs/{run}"));
    let post: serde_json::Value = serde_json::from_slice(
        &std::fs::read(directory.join("orientation-post.json")).expect("post"),
    )
    .expect("post JSON");
    let critic_path = directory.join("reports/fixture-critic.json");
    let original = std::fs::read(&critic_path).expect("Critic report");
    for relative in post["planning"]["run_artifacts"]
        .as_object()
        .expect("planning inventory")
        .keys()
    {
        let mut critic: serde_json::Value = serde_json::from_slice(&original).expect("Critic JSON");
        let path = format!(".shepherd/runs/{run}/{relative}");
        critic["evidence"]
            .as_array_mut()
            .expect("evidence")
            .retain(|entry| entry["path"] != path);
        std::fs::write(
            &critic_path,
            serde_json::to_vec(&critic).expect("omitted evidence"),
        )
        .expect("fixture report");
        let denied = invoke(&root, &["run", "transition", run, "--to", "planned"]);
        assert!(
            !denied.status.success(),
            "unreviewed artifact {relative} passed planned transition"
        );
        assert!(
            text(&denied.stderr).contains("Critic did not bind exact planning artifact")
                || text(&denied.stderr).contains("claim has unbound evidence"),
            "{}",
            text(&denied.stderr)
        );
        std::fs::write(&critic_path, &original).expect("restore report");
    }
    let accepted = invoke(&root, &["run", "transition", run, "--to", "planned"]);
    assert!(accepted.status.success(), "{}", text(&accepted.stderr));
    cleanup(&root);
}

fn commit_fixture_paths(root: &Path, paths: &[&str]) -> String {
    assert!(
        Command::new("git")
            .args(["add", "-f", "--"])
            .args(paths)
            .current_dir(root)
            .status()
            .expect("stage fixture")
            .success()
    );
    let commit = Command::new("git")
        .args([
            "-c",
            "user.name=Shepherd Tests",
            "-c",
            "user.email=shepherd-tests@example.invalid",
            "commit",
            "--quiet",
            "-m",
            "commit planning inputs",
        ])
        .current_dir(root)
        .output()
        .expect("commit fixture");
    assert!(commit.status.success(), "{}", text(&commit.stderr));
    let head = Command::new("git")
        .args(["rev-parse", "HEAD"])
        .current_dir(root)
        .output()
        .expect("HEAD");
    assert!(head.status.success());
    text(&head.stdout).trim().to_owned()
}

#[test]
fn planning_only_descendant_keeps_source_baseline_and_records_execution_head() {
    let root = fixture("planning-descendant");
    let run = "v915";
    let baseline = plan_fixture::prepare_execution(&root, run, &["lane-a"], 3);
    assert!(
        invoke(&root, &["run", "transition", run, "--to", "planted"])
            .status
            .success()
    );
    let head = commit_fixture_paths(
        &root,
        &[
            &format!(".shepherd/runs/{run}/plan-probes.json"),
            &format!(".shepherd/runs/{run}/reports/fixture-critic.json"),
        ],
    );
    assert_ne!(baseline, head);
    for args in [
        vec!["plan", "verify", "--run", run, "--json"],
        vec!["run", "transition", run, "--to", "planned"],
        vec!["sprint", "open", "--run", run],
    ] {
        let accepted = invoke(&root, &args);
        assert!(
            accepted.status.success(),
            "{args:?}: {}",
            text(&accepted.stderr)
        );
    }
    let directory = root.join(format!(".shepherd/runs/{run}"));
    let post: serde_json::Value = serde_json::from_slice(
        &std::fs::read(directory.join("orientation-post.json")).expect("post"),
    )
    .expect("post JSON");
    assert_eq!(post["planning"]["baseline"], baseline);
    let state = RunState::load(&directory.join("run.json")).expect("opened run");
    assert_eq!(state.extra["planning_execution_head"], head);
    cleanup(&root);
}

#[test]
fn planning_descendants_reject_product_seed_mesh_other_runs_and_unissued_reports() {
    for relative in [
        "src/plan-fixture-0.rs",
        ".shepherd/runs/v916/seed.md",
        ".shepherd/runs/v916/mesh.md",
        ".shepherd/runs/v916/reports/unissued.json",
        ".shepherd/runs/v917/reports/foreign.json",
    ] {
        let root = fixture("nonplanning-descendant");
        let run = "v916";
        plan_fixture::prepare_execution(&root, run, &["lane-a"], 3);
        assert!(
            invoke(&root, &["run", "transition", run, "--to", "planted"])
                .status
                .success()
        );
        let path = root.join(relative);
        std::fs::create_dir_all(path.parent().expect("fixture parent")).expect("fixture parent");
        let original = std::fs::read(&path).unwrap_or_default();
        let mut changed = original.clone();
        changed.extend_from_slice(b"\n// Nonplanning tracked change.\n");
        std::fs::write(&path, changed).expect("changed fixture");
        commit_fixture_paths(&root, &[relative]);
        let denied = invoke(&root, &["plan", "verify", "--run", run, "--json"]);
        assert!(
            !denied.status.success(),
            "non-planning descendant accepted {relative}"
        );
        assert!(
            text(&denied.stderr).contains("planning descendant changes non-planning path"),
            "{}",
            text(&denied.stderr)
        );
        if relative.starts_with("src/") {
            std::fs::write(path, original).expect("revert fixture product change");
            commit_fixture_paths(&root, &[relative]);
            let denied = invoke(&root, &["plan", "verify", "--run", run, "--json"]);
            assert!(
                !denied.status.success(),
                "reverted product history was treated as planning-only"
            );
            assert!(
                text(&denied.stderr).contains("planning descendant changes non-planning path"),
                "{}",
                text(&denied.stderr)
            );
        }
        cleanup(&root);
    }
}

#[test]
fn planning_baseline_rejects_unknown_noncommit_and_nonancestor_objects() {
    let root = fixture("planning-baseline-identity");
    let run = "v918";
    plan_fixture::prepare_execution(&root, run, &["lane-a"], 3);
    assert!(
        invoke(&root, &["run", "transition", run, "--to", "planted"])
            .status
            .success()
    );
    let tree = Command::new("git")
        .args(["rev-parse", "HEAD^{tree}"])
        .current_dir(&root)
        .output()
        .expect("tree");
    assert!(tree.status.success());
    let tree = text(&tree.stdout).trim().to_owned();
    let unrelated = Command::new("git")
        .args([
            "-c",
            "user.name=Shepherd Tests",
            "-c",
            "user.email=shepherd-tests@example.invalid",
            "commit-tree",
            &tree,
            "-m",
            "unrelated fixture root",
        ])
        .current_dir(&root)
        .output()
        .expect("unrelated commit object");
    assert!(unrelated.status.success(), "{}", text(&unrelated.stderr));
    let unrelated = text(&unrelated.stdout).trim().to_owned();
    let probes_path = root.join(format!(".shepherd/runs/{run}/plan-probes.json"));
    let original = std::fs::read(&probes_path).expect("probes");
    for (baseline, message) in [
        ("0".repeat(40), "not a known commit"),
        (tree, "not a known commit"),
        (unrelated, "not an ancestor"),
    ] {
        let mut probes: serde_json::Value = serde_json::from_slice(&original).expect("probe JSON");
        probes["baseline"] = baseline.into();
        std::fs::write(
            &probes_path,
            serde_json::to_vec(&probes).expect("invalid baseline"),
        )
        .expect("fixture probes");
        let denied = invoke(&root, &["plan", "verify", "--run", run, "--json"]);
        assert!(!denied.status.success(), "unverified baseline accepted");
        assert!(
            text(&denied.stderr).contains(message),
            "{}",
            text(&denied.stderr)
        );
    }
    cleanup(&root);
}

#[test]
fn execution_rejects_unknown_duplicate_or_nonpending_lane_registrations() {
    let root = fixture("planning-lane-custody");
    let run = "v910-dev0";
    plan_fixture::prepare_execution(&root, run, &["lane-a"], 3);
    let registered = invoke(
        &root,
        &[
            "run",
            "lane",
            "add",
            run,
            "lane-a",
            "--branch",
            "lane/retained",
        ],
    );
    assert!(registered.status.success(), "{}", text(&registered.stderr));
    let state_path = root.join(format!(".shepherd/runs/{run}/run.json"));
    let original = std::fs::read(&state_path).expect("preregistered pending lane");
    let state: serde_json::Value = serde_json::from_slice(&original).expect("lane state JSON");
    for (field, value) in [
        ("id", serde_json::json!("unplanned")),
        ("state", serde_json::json!("complete")),
        ("state", serde_json::json!("in-progress")),
        ("plan", serde_json::json!("lanes/foreign/plan.md")),
        ("accepted_commit", serde_json::json!("abc123")),
        ("merged", serde_json::json!(true)),
    ] {
        let mut changed = state.clone();
        changed["lanes"][0][field] = value;
        let bytes = serde_json::to_vec(&changed).expect("changed lane fixture");
        std::fs::write(&state_path, &bytes).expect("write lane fixture");
        let refused = invoke(&root, &["sprint", "open", "--run", run]);
        assert!(
            !refused.status.success(),
            "invalid pre-execution lane {field} was accepted"
        );
        assert_eq!(
            std::fs::read(&state_path).expect("unchanged invalid state"),
            bytes
        );
    }
    let mut duplicate = state.clone();
    duplicate["lanes"]
        .as_array_mut()
        .expect("lane rows")
        .push(state["lanes"][0].clone());
    let duplicate = serde_json::to_vec(&duplicate).expect("duplicate lane fixture");
    std::fs::write(&state_path, &duplicate).expect("write duplicate lanes");
    let refused = invoke(&root, &["sprint", "open", "--run", run]);
    assert!(
        !refused.status.success(),
        "duplicate pre-execution lane was accepted"
    );
    assert_eq!(
        std::fs::read(&state_path).expect("unchanged duplicate state"),
        duplicate
    );

    std::fs::write(&state_path, original).expect("restore native pending registration");
    let opened = invoke(&root, &["sprint", "open", "--run", run]);
    assert!(opened.status.success(), "{}", text(&opened.stderr));
    let state = RunState::load(&state_path).expect("opened lane state");
    assert_eq!(state.lanes.len(), 1);
    assert_eq!(state.lanes[0].branch, "lane/retained");
    assert_eq!(state.lanes[0].state, Vocabulary::Known(LaneStatus::Pending));
    cleanup(&root);
}

#[test]
fn linked_worktree_reads_and_mutates_only_the_primary_runs_root() {
    let root = fixture("linked-primary");
    let init = invoke(&root, &["run", "init", "v906-dev0"]);
    assert_eq!(init.status.code(), Some(0));
    let commit = Command::new("git")
        .args([
            "-c",
            "user.name=Shepherd Test",
            "-c",
            "user.email=shepherd-test@example.invalid",
            "commit",
            "--allow-empty",
            "--quiet",
            "-m",
            "fixture",
        ])
        .current_dir(&root)
        .status()
        .expect("commit fixture");
    assert!(commit.success());
    let linked = root.with_file_name(format!(
        "{}-linked",
        root.file_name().expect("fixture name").to_string_lossy()
    ));
    let add = Command::new("git")
        .args(["worktree", "add", "--detach", "--quiet"])
        .arg(&linked)
        .arg("HEAD")
        .current_dir(&root)
        .status()
        .expect("add linked worktree");
    assert!(add.success());
    std::fs::create_dir_all(linked.join(".shepherd/runs/v999-dev0")).expect("linked shadow");
    std::fs::write(
        linked.join(".shepherd/runs/v999-dev0/run.json"),
        b"{\"run\":\"v999-dev0\"}\n",
    )
    .expect("linked shadow state");
    let shown = invoke(&linked, &["run", "show", "v906-dev0"]);
    assert_eq!(
        shown.status.code(),
        Some(0),
        "stderr={}",
        text(&shown.stderr)
    );
    let shadow = invoke(&linked, &["run", "show", "v999-dev0"]);
    assert_eq!(shadow.status.code(), Some(5));
    let update = invoke(
        &linked,
        &["run", "set", "v906-dev0", "--branch", "linked-update"],
    );
    assert_eq!(
        update.status.code(),
        Some(0),
        "stderr={}",
        text(&update.stderr)
    );
    assert!(
        std::fs::read_to_string(root.join(".shepherd/runs/v906-dev0/run.json"))
            .expect("primary state")
            .contains("\"linked-update\"")
    );
    std::fs::remove_dir_all(&linked).expect("remove linked fixture");
    cleanup(&root);
}