@opengsd/gsd-pi 1.3.0-dev.eed73bea → 1.4.0

package/src/resources/extensions/gsd/tests/db-memory-fts-schema.test.ts

@@ -3,11 +3,16 @@
 
 import { describe, test } from "node:test";
 import assert from "node:assert/strict";
+import { createRequire } from "node:module";
 import {
+  MEMORIES_FTS_REBUILT_KEY,
   isMemoriesFtsAvailableSchema,
+  rebuildMemoriesFtsSchemaOnce,
   tryCreateMemoriesFtsSchema,
 } from "../db-memory-fts-schema.ts";
-import type { DbAdapter, DbStatement } from "../db-adapter.ts";
+import { createDbAdapter, type DbAdapter, type DbStatement } from "../db-adapter.ts";
+
+const _require = createRequire(import.meta.url);
 
 class FakeStatement implements DbStatement {
   private readonly row: Record<string, unknown> | undefined;
@@ -32,6 +37,7 @@ class FakeStatement implements DbStatement {
 class FakeAdapter implements DbAdapter {
   readonly execCalls: string[] = [];
   hasFts = false;
+  hasRebuildMarker = false;
   failExec = false;
 
   exec(sql: string): void {
@@ -39,13 +45,26 @@ class FakeAdapter implements DbAdapter {
     if (this.failExec) throw new Error("fts unavailable");
   }
 
-  prepare(): DbStatement {
-    return new FakeStatement(this.hasFts ? { name: "memories_fts" } : undefined);
+  prepare(sql: string): DbStatement {
+    if (sql.includes("sqlite_master")) {
+      return new FakeStatement(this.hasFts ? { name: "memories_fts" } : undefined);
+    }
+    if (sql.includes("runtime_kv")) {
+      return new FakeStatement(this.hasRebuildMarker ? { present: 1 } : undefined);
+    }
+    return new FakeStatement(undefined);
   }
 
   close(): void {}
 }
 
+function openMemoryAdapter(): { db: DbAdapter; close: () => void } {
+  const sqlite = _require("node:sqlite") as { DatabaseSync: new (path: string) => unknown };
+  const raw = new sqlite.DatabaseSync(":memory:");
+  const db = createDbAdapter(raw);
+  return { db, close: () => db.close() };
+}
+
 describe("db-memory-fts-schema", () => {
   test("creates memories_fts and insert/delete/update triggers", () => {
     const db = new FakeAdapter();
@@ -83,4 +102,40 @@ describe("db-memory-fts-schema", () => {
     db.hasFts = true;
     assert.equal(isMemoriesFtsAvailableSchema(db), true);
   });
+
+  test("rebuilds the external-content index once and records a marker", () => {
+    const { db, close } = openMemoryAdapter();
+    try {
+      db.exec("CREATE TABLE memories (seq INTEGER PRIMARY KEY AUTOINCREMENT, content TEXT NOT NULL)");
+      db.exec("INSERT INTO memories (content) VALUES ('pre FTS auth memory must be searchable')");
+
+      const ok = tryCreateMemoriesFtsSchema(db);
+      if (!ok) return;
+
+      const before = db.prepare("SELECT rowid FROM memories_fts WHERE memories_fts MATCH 'auth'").all();
+      assert.equal(before.length, 0, "external-content FTS starts empty for existing rows");
+
+      rebuildMemoriesFtsSchemaOnce(db);
+
+      const after = db.prepare("SELECT rowid FROM memories_fts WHERE memories_fts MATCH 'auth'").all();
+      assert.deepEqual(after.map((row) => row["rowid"]), [1]);
+      const marker = db.prepare(
+        "SELECT value_json FROM runtime_kv WHERE scope = 'global' AND scope_id = '' AND key = :key",
+      ).get({ ":key": MEMORIES_FTS_REBUILT_KEY });
+      assert.ok(marker, "rebuild marker should be stored");
+    } finally {
+      close();
+    }
+  });
+
+  test("skips rebuild when marker already exists", () => {
+    const db = new FakeAdapter();
+    db.hasFts = true;
+    db.hasRebuildMarker = true;
+
+    rebuildMemoriesFtsSchemaOnce(db);
+
+    assert.ok(db.execCalls.some((sql) => sql.includes("CREATE TABLE IF NOT EXISTS runtime_kv")));
+    assert.ok(!db.execCalls.some((sql) => sql.includes("VALUES('rebuild')")));
+  });
 });

package/src/resources/extensions/gsd/tests/decisions-projection-from-memories.test.ts

@@ -142,6 +142,57 @@ test("backfill is idempotent — re-running over migrated rows is a no-op", () =
   }
 });
 
+test("backfill skips a decision whose memory insert throws and continues later rows", () => {
+  const base = makeTmpBase();
+  try {
+    seedRawDecision({
+      id: "D001",
+      when_context: "M001",
+      scope: "M001",
+      decision: "before poison",
+      choice: "A",
+      rationale: "first row",
+    });
+    seedRawDecision({
+      id: "D002",
+      when_context: "M001",
+      scope: "M001",
+      decision: "poison",
+      choice: "B",
+      rationale: "this insert throws",
+    });
+    seedRawDecision({
+      id: "D003",
+      when_context: "M001",
+      scope: "M001",
+      decision: "after poison",
+      choice: "C",
+      rationale: "tail row",
+    });
+
+    const adapter = _getAdapter();
+    assert.ok(adapter);
+    adapter.exec(`
+      CREATE TRIGGER fail_d002_memory_insert
+      BEFORE INSERT ON memories
+      WHEN json_extract(NEW.structured_fields, '$.sourceDecisionId') = 'D002'
+      BEGIN
+        SELECT RAISE(ABORT, 'poison decision D002');
+      END
+    `);
+
+    const written = backfillDecisionsToMemories();
+    assert.equal(written, 2, "one poisoned row should not abort the batch");
+    assert.deepEqual(
+      getAllDecisionsFromMemories().map((d) => d.id),
+      ["D001", "D003"],
+      "rows after the poisoned decision should still be migrated",
+    );
+  } finally {
+    cleanup(base);
+  }
+});
+
 // ─── Drift auto-heal ───────────────────────────────────────────────────────
 
 test("backfill auto-heals when a source decision's superseded_by changes after migration", () => {

package/src/resources/extensions/gsd/tests/destructive-guard.test.ts

@@ -0,0 +1,44 @@
+import test from "node:test";
+import assert from "node:assert/strict";
+
+import { classifyCommand } from "../safety/destructive-guard.ts";
+
+test("destructive guard ignores rm -rf text inside quoted literals and comments", () => {
+  const readOnlyCommands = [
+    'grep -rn "rm -rf" .',
+    'echo "rm -rf /tmp/x"',
+    'git commit -m "remove stray rm -rf usage"',
+    "cat notes.md  # remove stray rm -rf usage",
+    'printf "rm -rf /tmp/x\\n"',
+  ];
+
+  for (const command of readOnlyCommands) {
+    assert.deepEqual(classifyCommand(command), { destructive: false, labels: [] }, command);
+  }
+});
+
+test("destructive guard still detects direct and wrapper-prefixed recursive deletes", () => {
+  const destructiveCommands = [
+    "rm -rf build",
+    "rm build -rf",
+    "sudo rm -rf /",
+    "doas rm -rf /",
+    "sudo -u bob rm -rf /x",
+    "timeout 5 rm -rf /x",
+    "time rm -rf build",
+    "find . -exec rm -rf {} \\;",
+    "cat doomed.txt | xargs rm -rf /tmp/x",
+    'rm -rf "/tmp/my build"',
+  ];
+
+  for (const command of destructiveCommands) {
+    assert.deepEqual(classifyCommand(command), {
+      destructive: true,
+      labels: ["recursive delete"],
+    }, command);
+  }
+});
+
+test("destructive guard treats quoted interpreter payloads as literals", () => {
+  assert.deepEqual(classifyCommand('bash -c "rm -rf /"'), { destructive: false, labels: [] });
+});

package/src/resources/extensions/gsd/tests/dispatch-missing-task-plans.test.ts

@@ -96,6 +96,40 @@ function scaffoldMilestoneContext(basePath: string, mid: string): void {
   ].join("\n"));
 }
 
+function scaffoldLegacyMilestoneContext(basePath: string, mid: string): void {
+  const dir = join(basePath, ".gsd", "milestones", mid);
+  mkdirSync(dir, { recursive: true });
+  writeFileSync(join(dir, `${mid}-CONTEXT.md`), [
+    `# ${mid}: Test Milestone`,
+    "",
+    "Context for legacy dispatch recovery tests.",
+    "",
+  ].join("\n"));
+}
+
+function scaffoldLegacySlicePlan(basePath: string, mid: string, sid: string): void {
+  const dir = join(basePath, ".gsd", "milestones", mid, "slices", sid);
+  mkdirSync(join(dir, "tasks"), { recursive: true });
+  writeFileSync(join(dir, `${sid}-PLAN.md`), [
+    `# ${sid}: Legacy Slice`,
+    "",
+    "## Tasks",
+    "- T01: Do something",
+    "",
+  ].join("\n"));
+}
+
+function scaffoldLegacyTaskPlan(basePath: string, mid: string, sid: string, tid: string): void {
+  const dir = join(basePath, ".gsd", "milestones", mid, "slices", sid, "tasks");
+  mkdirSync(dir, { recursive: true });
+  writeFileSync(join(dir, `${tid}-PLAN.md`), [
+    `# ${tid}: First Task`,
+    "",
+    "Implement the task.",
+    "",
+  ].join("\n"));
+}
+
 function scaffoldTaskPlan(basePath: string, mid: string, sid: string, tid: string): void {
   // Flat-phase: no per-task plan files. This is a no-op — tasks live as
   // checkboxes inside the slice plan. Kept for backward-compat with tests
@@ -167,6 +201,115 @@ test("dispatch: present task plan proceeds to execute-task normally", async (t)
     `unitId should be M002/S03/T01, got: ${result.action === "dispatch" ? result.unitId : "(stop)"}`);
 });
 
+test("dispatch: missing legacy task plan recovery increments a per-slice retry counter", async (t) => {
+  const tmp = mkdtempSync(join(tmpdir(), "gsd-1087-retry-"));
+  t.after(() => rmSync(tmp, { recursive: true, force: true }));
+
+  scaffoldLegacyMilestoneContext(tmp, "M002");
+  scaffoldLegacySlicePlan(tmp, "M002", "S03");
+
+  const session = {
+    missingTaskPlanRetryCount: new Map<string, number>(),
+  };
+  const result = await resolveDispatch(makeContextFor(tmp, "M002", "S03", "T01", session));
+
+  assert.equal(result.action, "dispatch");
+  assert.ok(result.action === "dispatch" && result.unitType === "plan-slice",
+    `unitType should be plan-slice, got: ${result.action === "dispatch" ? result.unitType : "(stop)"}`);
+  assert.ok(result.action === "dispatch" && result.unitId === "M002/S03",
+    `unitId should be M002/S03, got: ${result.action === "dispatch" ? result.unitId : "(stop)"}`);
+  assert.equal(session.missingTaskPlanRetryCount.get("M002/S03"), 1);
+});
+
+test("dispatch: missing legacy task plan recovery stops when retry counter is exhausted", async (t) => {
+  const tmp = mkdtempSync(join(tmpdir(), "gsd-1087-stop-"));
+  t.after(() => rmSync(tmp, { recursive: true, force: true }));
+
+  scaffoldLegacyMilestoneContext(tmp, "M002");
+  scaffoldLegacySlicePlan(tmp, "M002", "S03");
+
+  const session = {
+    missingTaskPlanRetryCount: new Map<string, number>([["M002/S03", 2]]),
+  };
+  const result = await resolveDispatch(makeContextFor(tmp, "M002", "S03", "T01", session));
+
+  assert.equal(result.action, "stop");
+  assert.ok(result.action === "stop");
+  assert.equal(result.level, "error");
+  assert.match(result.reason, /Missing task-plan recovery failed 2 times for M002\/S03/);
+  assert.match(result.reason, /manual intervention required/);
+  assert.equal(session.missingTaskPlanRetryCount.has("M002/S03"), false);
+});
+
+test("dispatch: present legacy task plan clears missing-plan recovery retry counter", async (t) => {
+  const tmp = mkdtempSync(join(tmpdir(), "gsd-1087-clear-"));
+  t.after(() => rmSync(tmp, { recursive: true, force: true }));
+
+  scaffoldLegacyMilestoneContext(tmp, "M002");
+  scaffoldLegacySlicePlan(tmp, "M002", "S03");
+  scaffoldLegacyTaskPlan(tmp, "M002", "S03", "T01");
+
+  const session = {
+    missingTaskPlanRetryCount: new Map<string, number>([["M002/S03", 1]]),
+    preExecRetryCount: new Map<string, number>([["M002/S03", 2]]),
+  };
+  const result = await resolveDispatch(makeContextFor(tmp, "M002", "S03", "T01", session));
+
+  assert.equal(result.action, "dispatch");
+  assert.ok(result.action === "dispatch" && result.unitType === "execute-task",
+    `unitType should be execute-task, got: ${result.action === "dispatch" ? result.unitType : "(stop)"}`);
+  assert.equal(session.missingTaskPlanRetryCount.has("M002/S03"), false);
+  assert.equal(session.preExecRetryCount.get("M002/S03"), 2,
+    "pre-exec retry counter must not be cleared when task plan is present");
+});
+
+test("dispatch: missing-task-plan recovery loop terminates even when the shared pre-exec key is reset between rounds (#1087)", async (t) => {
+  // The recovery rule re-dispatches plan-slice with unitId "${mid}/${sid}".
+  // That regenerated plan-slice carries the same currentUnit.id, and on a
+  // pre-execution pass the post-unit hook deletes that key from
+  // preExecRetryCount (auto-post-unit.ts). Missing per-task PLAN projection
+  // files do not fail pre-exec checks, so the regenerated plan-slice typically
+  // passes and that delete fires every cycle. If recovery shared
+  // preExecRetryCount, its counter would be wiped to 0 each round and the loop
+  // would never reach the cap. Here we simulate that reset between rounds and
+  // assert the dedicated counter still climbs to MAX and stops.
+  const tmp = mkdtempSync(join(tmpdir(), "gsd-1087-loop-term-"));
+  t.after(() => rmSync(tmp, { recursive: true, force: true }));
+
+  scaffoldLegacyMilestoneContext(tmp, "M002");
+  scaffoldLegacySlicePlan(tmp, "M002", "S03");
+
+  const session = {
+    missingTaskPlanRetryCount: new Map<string, number>(),
+    preExecRetryCount: new Map<string, number>(),
+  };
+
+  // Round 1: missing task plan → recover (counter 0 → 1).
+  const r1 = await resolveDispatch(makeContextFor(tmp, "M002", "S03", "T01", session));
+  assert.ok(r1.action === "dispatch" && r1.unitType === "plan-slice",
+    `round 1 should re-dispatch plan-slice, got: ${r1.action === "dispatch" ? r1.unitType : "(stop)"}`);
+  assert.equal(session.missingTaskPlanRetryCount.get("M002/S03"), 1);
+
+  // The regenerated plan-slice passes its post-unit pre-exec check, deleting
+  // the shared "${mid}/${sid}" key from preExecRetryCount.
+  session.preExecRetryCount.delete("M002/S03");
+
+  // Round 2: still missing → recover (counter 1 → 2), unaffected by the reset.
+  const r2 = await resolveDispatch(makeContextFor(tmp, "M002", "S03", "T01", session));
+  assert.ok(r2.action === "dispatch" && r2.unitType === "plan-slice",
+    `round 2 should re-dispatch plan-slice, got: ${r2.action === "dispatch" ? r2.unitType : "(stop)"}`);
+  assert.equal(session.missingTaskPlanRetryCount.get("M002/S03"), 2);
+
+  session.preExecRetryCount.delete("M002/S03");
+
+  // Round 3: cap reached → stop. The loop terminates despite the resets.
+  const r3 = await resolveDispatch(makeContextFor(tmp, "M002", "S03", "T01", session));
+  assert.equal(r3.action, "stop");
+  assert.ok(r3.action === "stop" && r3.level === "error");
+  assert.match(r3.reason, /Missing task-plan recovery failed 2 times for M002\/S03/);
+  assert.equal(session.missingTaskPlanRetryCount.has("M002/S03"), false);
+});
+
 test("dispatch: session milestone mismatch stops before missing-task-plan recovery", async (t) => {
   const tmp = mkdtempSync(join(tmpdir(), "gsd-session-milestone-mismatch-"));
   t.after(() => rmSync(tmp, { recursive: true, force: true }));

package/src/resources/extensions/gsd/tests/doctor-scope-db-unavailable.test.ts

@@ -1,12 +1,22 @@
 import { afterEach, test } from "node:test";
 import assert from "node:assert/strict";
-import { _getAdapter, closeDatabase, insertMilestone, openDatabase } from "../gsd-db.ts";
-import { mkdtempSync, mkdirSync, rmSync, writeFileSync } from "node:fs";
+import {
+  _getAdapter,
+  closeDatabase,
+  insertArtifact,
+  insertMilestone,
+  insertSlice,
+  insertTask,
+  openDatabase,
+} from "../gsd-db.ts";
+import { mkdtempSync, mkdirSync, readFileSync, rmSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 import { filterDoctorIssues } from "../doctor-format.ts";
 import { checkEngineHealth } from "../doctor-engine-checks.ts";
+import { MEMORIES_FTS_REBUILT_KEY } from "../db-memory-fts-schema.ts";
 import { appendEvent } from "../workflow-events.ts";
+import { renderPlanFromDb, renderRoadmapFromDb } from "../markdown-renderer.ts";
 
 afterEach(() => {
   closeDatabase();
@@ -61,6 +71,139 @@ test("checkEngineHealth reports db_unavailable when gsd.db exists but the DB is
   assert.equal(dbIssue.file, ".gsd/gsd.db");
 });
 
+test("checkEngineHealth reports memories_fts without the rebuild marker", async (t) => {
+  const base = mkdtempSync(join(tmpdir(), "gsd-doctor-memory-fts-marker-"));
+  t.after(() => rmSync(base, { recursive: true, force: true }));
+
+  const gsdDir = join(base, ".gsd");
+  mkdirSync(gsdDir, { recursive: true });
+
+  openDatabase(join(gsdDir, "gsd.db"));
+  const adapter = _getAdapter()!;
+  const fts = adapter.prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='memories_fts'").get();
+  if (!fts) return;
+
+  adapter.prepare(
+    "DELETE FROM runtime_kv WHERE scope = 'global' AND scope_id = '' AND key = :key",
+  ).run({ ":key": MEMORIES_FTS_REBUILT_KEY });
+
+  const issues: any[] = [];
+  await checkEngineHealth(base, issues, []);
+
+  const ftsIssue = issues.find((issue) => issue.code === "memories_fts_rebuild_missing");
+  assert.ok(ftsIssue, "doctor should surface a potentially desynced memory FTS index");
+  assert.equal(ftsIssue.severity, "warning");
+  assert.equal(ftsIssue.unitId, "project");
+  assert.equal(ftsIssue.file, ".gsd/gsd.db");
+  assert.equal(ftsIssue.fixable, false);
+});
+
+test("checkEngineHealth reports checkbox divergence against DB status", async (t) => {
+  const base = mkdtempSync(join(tmpdir(), "gsd-doctor-checkbox-drift-"));
+  t.after(() => rmSync(base, { recursive: true, force: true }));
+
+  const gsdDir = join(base, ".gsd");
+  mkdirSync(gsdDir, { recursive: true });
+
+  openDatabase(join(gsdDir, "gsd.db"));
+  insertMilestone({ id: "M001", title: "Foundation", status: "active" });
+  insertSlice({ id: "S01", milestoneId: "M001", title: "Slice", status: "pending", risk: "low", depends: [], sequence: 1 });
+  insertTask({ id: "T01", milestoneId: "M001", sliceId: "S01", title: "Task", status: "complete", sequence: 1 });
+
+  const roadmap = await renderRoadmapFromDb(base, "M001");
+  if ("skipped" in roadmap) assert.fail("planned milestone should render a roadmap");
+  const plan = await renderPlanFromDb(base, "M001", "S01");
+
+  writeFileSync(roadmap.roadmapPath, readFileSync(roadmap.roadmapPath, "utf-8").replace("- [ ] **S01:", "- [x] **S01:"), "utf-8");
+  writeFileSync(plan.planPath, readFileSync(plan.planPath, "utf-8").replace("- [x] **T01**:", "- [ ] **T01**:"), "utf-8");
+
+  const issues: any[] = [];
+  await checkEngineHealth(base, issues, []);
+
+  const divergences = issues.filter((issue) => issue.code === "checkbox_db_status_divergence");
+  assert.deepEqual(
+    divergences.map((issue) => issue.unitId).sort(),
+    ["M001/S01", "M001/S01/T01"],
+  );
+});
+
+test("checkEngineHealth keeps PLAN checkbox divergence after stale projection flush", async (t) => {
+  const base = mkdtempSync(join(tmpdir(), "gsd-doctor-checkbox-plan-drift-"));
+  t.after(() => rmSync(base, { recursive: true, force: true }));
+
+  const gsdDir = join(base, ".gsd");
+  mkdirSync(gsdDir, { recursive: true });
+
+  openDatabase(join(gsdDir, "gsd.db"));
+  insertMilestone({ id: "M001", title: "Foundation", status: "active" });
+  insertSlice({ id: "S01", milestoneId: "M001", title: "Slice", status: "pending", risk: "low", depends: [], sequence: 1 });
+  insertTask({ id: "T01", milestoneId: "M001", sliceId: "S01", title: "Task", status: "complete", sequence: 1 });
+
+  const roadmap = await renderRoadmapFromDb(base, "M001");
+  if ("skipped" in roadmap) assert.fail("planned milestone should render a roadmap");
+  const plan = await renderPlanFromDb(base, "M001", "S01");
+
+  writeFileSync(roadmap.roadmapPath, readFileSync(roadmap.roadmapPath, "utf-8").replace("- [ ] **S01:", "- [x] **S01:"), "utf-8");
+  writeFileSync(plan.planPath, readFileSync(plan.planPath, "utf-8").replace("- [x] **T01**:", "- [ ] **T01**:"), "utf-8");
+  appendEvent(base, {
+    cmd: "complete-task",
+    params: { milestoneId: "M001", sliceId: "S01", taskId: "T01" },
+    ts: "2999-01-01T00:00:00.000Z",
+    actor: "agent",
+  });
+
+  const issues: any[] = [];
+  const fixes: string[] = [];
+  await checkEngineHealth(base, issues, fixes);
+
+  const divergences = issues.filter((issue) => issue.code === "checkbox_db_status_divergence");
+  assert.deepEqual(
+    divergences.map((issue) => issue.unitId),
+    ["M001/S01/T01"],
+    "stale ROADMAP divergence is cleared after re-render, but stale PLAN task divergence remains",
+  );
+  assert.ok(fixes.includes("re-rendered stale projections for M001"));
+  assert.match(readFileSync(plan.planPath, "utf-8"), /- \[ \] \*\*T01\*\*:/);
+});
+
+test("checkEngineHealth reads task checkboxes from the <tasks> block, not a stray line above it", async (t) => {
+  const base = mkdtempSync(join(tmpdir(), "gsd-doctor-task-section-"));
+  t.after(() => rmSync(base, { recursive: true, force: true }));
+
+  const gsdDir = join(base, ".gsd");
+  mkdirSync(gsdDir, { recursive: true });
+
+  openDatabase(join(gsdDir, "gsd.db"));
+  insertMilestone({ id: "M001", title: "Foundation", status: "active" });
+  insertSlice({ id: "S01", milestoneId: "M001", title: "Slice", status: "pending", risk: "low", depends: [], sequence: 1 });
+  insertTask({ id: "T01", milestoneId: "M001", sliceId: "S01", title: "Task", status: "complete", sequence: 1 });
+
+  const roadmap = await renderRoadmapFromDb(base, "M001");
+  if ("skipped" in roadmap) assert.fail("planned milestone should render a roadmap");
+  const plan = await renderPlanFromDb(base, "M001", "S01");
+
+  // Flip the authoritative <tasks> checkbox so it disagrees with the DB
+  // (DB: complete, markdown: unchecked = real drift), then inject a *checked*
+  // decoy line for the same task above the <tasks> block. The old whole-file
+  // regex matched the decoy first and hid the real drift; parsePlan reads the
+  // authoritative <tasks> block and still reports it. No events are appended,
+  // so the projection-drift re-render never runs and the crafted file stands.
+  const rendered = readFileSync(plan.planPath, "utf-8")
+    .replace("- [x] **T01**:", "- [ ] **T01**:")
+    .replace("<tasks>\n", "- [x] **T01**: stale duplicate above the tasks block\n\n<tasks>\n");
+  writeFileSync(plan.planPath, rendered, "utf-8");
+
+  const issues: any[] = [];
+  await checkEngineHealth(base, issues, []);
+
+  const divergences = issues.filter((issue) => issue.code === "checkbox_db_status_divergence");
+  assert.deepEqual(
+    divergences.map((issue) => issue.unitId),
+    ["M001/S01/T01"],
+    "task drift must be read from the authoritative <tasks> block, not a stray checkbox above it",
+  );
+});
+
 test("checkEngineHealth reads canonical reopen events from worktree bases", async (t) => {
   const base = mkdtempSync(join(tmpdir(), "gsd-doctor-reopen-worktree-"));
   t.after(() => rmSync(base, { recursive: true, force: true }));
@@ -149,3 +292,97 @@ test("checkEngineHealth treats explicit reopen as authoritative when dispatch ti
     "explicit reopen should exempt reopened milestone even when completion dispatch timestamps are absent",
   );
 });
+
+test("checkEngineHealth reports artifact rows whose files are missing on disk", async (t) => {
+  const base = mkdtempSync(join(tmpdir(), "gsd-doctor-missing-artifact-"));
+  t.after(() => rmSync(base, { recursive: true, force: true }));
+
+  const gsdDir = join(base, ".gsd");
+  const worktree = join(gsdDir, "worktrees", "M001");
+  mkdirSync(join(worktree, ".gsd", "milestones", "M001"), { recursive: true });
+  writeFileSync(join(worktree, ".git"), "gitdir: ../../../../.git/worktrees/M001\n", "utf-8");
+  writeFileSync(join(worktree, ".gsd", "milestones", "M001", "M001-CONTEXT.md"), "# Context\n", "utf-8");
+
+  openDatabase(join(gsdDir, "gsd.db"));
+  insertArtifact({
+    path: "milestones/M001/M001-CONTEXT.md",
+    artifact_type: "CONTEXT",
+    milestone_id: "M001",
+    slice_id: null,
+    task_id: null,
+    full_content: "# Context\n",
+  });
+  insertArtifact({
+    path: "milestones/M001/M001-MISSING.md",
+    artifact_type: "CONTEXT",
+    milestone_id: "M001",
+    slice_id: null,
+    task_id: null,
+    full_content: "# Missing\n",
+  });
+
+  const issues: any[] = [];
+  await checkEngineHealth(worktree, issues, []);
+
+  assert.equal(
+    issues.some((issue) => issue.code === "artifact_file_missing" && issue.file === "milestones/M001/M001-CONTEXT.md"),
+    false,
+    "worktree-local artifacts should resolve through the projection root",
+  );
+  const missing = issues.find((issue) => issue.code === "artifact_file_missing" && issue.file === "milestones/M001/M001-MISSING.md");
+  assert.ok(missing, "missing artifact rows should be reported");
+  assert.equal(missing.unitId, "M001");
+  assert.equal(missing.fixable, false);
+});
+
+test("checkEngineHealth clears artifact_file_missing after projection re-render recreates the file", async (t) => {
+  const base = mkdtempSync(join(tmpdir(), "gsd-doctor-stale-missing-artifact-"));
+  t.after(() => rmSync(base, { recursive: true, force: true }));
+
+  const gsdDir = join(base, ".gsd");
+  mkdirSync(gsdDir, { recursive: true });
+
+  openDatabase(join(gsdDir, "gsd.db"));
+  insertMilestone({ id: "M001", title: "Foundation", status: "active", planning: { vision: "Ship the foundation." } });
+  insertSlice({ id: "S01", milestoneId: "M001", title: "Slice", status: "pending", risk: "low", depends: [], sequence: 1 });
+  insertArtifact({
+    path: "phases/01-foundation/01-ROADMAP.md",
+    artifact_type: "ROADMAP",
+    milestone_id: "M001",
+    slice_id: null,
+    task_id: null,
+    full_content: "# stale row only\n",
+  });
+  // CONTEXT is not re-rendered by flushWorkflowProjections, so its missing-file
+  // diagnostic must survive the post-re-render cleanup (guards against the
+  // clearing logic over-broadening to artifacts the same run did not recreate).
+  insertArtifact({
+    path: "phases/01-foundation/01-CONTEXT.md",
+    artifact_type: "CONTEXT",
+    milestone_id: "M001",
+    slice_id: null,
+    task_id: null,
+    full_content: "# stale context row only\n",
+  });
+  appendEvent(base, {
+    cmd: "plan-milestone",
+    params: { milestoneId: "M001" },
+    ts: "2999-01-01T00:00:00.000Z",
+    actor: "agent",
+  });
+
+  const issues: any[] = [];
+  const fixes: string[] = [];
+  await checkEngineHealth(base, issues, fixes);
+
+  assert.ok(fixes.includes("re-rendered missing projections for M001"));
+  assert.equal(
+    issues.some((issue) => issue.code === "artifact_file_missing" && issue.file === "phases/01-foundation/01-ROADMAP.md"),
+    false,
+    "doctor should not report a missing artifact that projection repair recreated in the same run",
+  );
+  assert.ok(
+    issues.some((issue) => issue.code === "artifact_file_missing" && issue.file === "phases/01-foundation/01-CONTEXT.md"),
+    "doctor should still report a missing artifact that projection repair did not recreate",
+  );
+});

package/src/resources/extensions/gsd/tests/exec-sandbox.test.ts

@@ -7,6 +7,7 @@ import { existsSync, mkdtempSync, mkdirSync, readFileSync, rmSync } from 'node:f
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 
+import { getShellConfig } from '@gsd/pi-coding-agent';
 import { EXEC_DEFAULTS, runExecSandbox, type ExecSandboxOptions } from '../exec-sandbox.ts';
 import { buildExecOptions, executeGsdExec } from '../tools/exec-tool.ts';
 import { isContextModeEnabled } from '../preferences-types.ts';
@@ -53,6 +54,21 @@ test('runExecSandbox: captures stdout, persists artifacts, returns digest', asyn
   }
 });
 
+test('runExecSandbox: bash runtime uses resolved shell config', async () => {
+  const base = freshBase();
+  try {
+    const { shell } = getShellConfig();
+    const result = await runExecSandbox(
+      { runtime: 'bash', script: 'printf "%s" "$0"' },
+      baseOpts(base),
+    );
+    assert.equal(result.exit_code, 0);
+    assert.equal(readFileSync(result.stdout_path, 'utf-8'), shell);
+  } finally {
+    cleanup(base);
+  }
+});
+
 test('runExecSandbox: persists optional request metadata', async () => {
   const base = freshBase();
   try {