@opengsd/gsd-pi 1.3.0-dev.65546769 → 1.3.0-dev.738160b9

package/src/resources/extensions/gsd/tests/orchestrator-logs.test.ts

@@ -36,6 +36,7 @@ import {
 import { resolveExpectedArtifactPath } from "../auto-artifact-paths.ts";
 import { AutoSession } from "../auto/session.ts";
 import { acquireSessionLock, releaseSessionLock } from "../session-lock.ts";
+import { clearGSDPreferencesCache } from "../preferences.ts";
 import { invalidateAllCaches } from "../cache.ts";
 import { invalidateStateCache } from "../state.ts";
 import {
@@ -63,12 +64,15 @@ interface FixtureOptions {
   dispatch?: UnifiedRule["where"];
   /** Drop the gate_runs table after seeding so emitUokGate's insertGateRun throws (:538 path). */
   dropGateRuns?: boolean;
+  /** Write project preferences that disable UOK gate telemetry. */
+  disableUokGates?: boolean;
 }
 
 interface Fixture {
   base: string;
   session: AutoSession;
   orchestrator: ReturnType<typeof createAutoOrchestrator>;
+  getAvailableCalls(): number;
   cleanup(): void;
 }
 
@@ -82,6 +86,7 @@ function makeFixture(opts: FixtureOptions = {}): Fixture {
 
   invalidateAllCaches();
   invalidateStateCache();
+  clearGSDPreferencesCache();
   openDatabase(join(base, ".gsd", "gsd.db"));
   insertMilestone({ id: "M001", title: "Milestone", status: "active" });
   insertSlice({ id: "S01", milestoneId: "M001", title: "Slice", status: "active", risk: "low", depends: [], demo: "", sequence: 1 });
@@ -100,6 +105,13 @@ function makeFixture(opts: FixtureOptions = {}): Fixture {
     join(sliceDir, "S01-PLAN.md"),
     ["# S01: Slice", "", "**Goal:** g", "**Demo:** d", "", "## Tasks", "", "- [ ] **T01: Task** `est:1h`", ""].join("\n"),
   );
+  if (opts.disableUokGates) {
+    writeFileSync(
+      join(base, ".gsd", "PREFERENCES.md"),
+      "---\nuok:\n  gates:\n    enabled: false\n---\n",
+    );
+    clearGSDPreferencesCache();
+  }
 
   acquireSessionLock(base);
 
@@ -112,8 +124,19 @@ function makeFixture(opts: FixtureOptions = {}): Fixture {
   session.currentMilestoneId = "M001";
   session.resourceVersionOnStart = null;
 
+  let getAvailableCalls = 0;
   const ctx: OrchestratorContext = {
-    ctx: { model: {}, modelRegistry: { getAll: () => [], getAvailable: () => [] }, ui: { notify() {} } } as never,
+    ctx: {
+      model: {},
+      modelRegistry: {
+        getAll: () => [],
+        getAvailable: () => {
+          getAvailableCalls += 1;
+          return [];
+        },
+      },
+      ui: { notify() {} },
+    } as never,
     pi: { getActiveTools: () => [] } as never,
     dispatchBasePath: base,
     runtimeBasePath: base,
@@ -140,8 +163,10 @@ function makeFixture(opts: FixtureOptions = {}): Fixture {
     base,
     session,
     orchestrator,
+    getAvailableCalls: () => getAvailableCalls,
     cleanup() {
       resetRegistry();
+      clearGSDPreferencesCache();
       try { releaseSessionLock(base); } catch { /* */ }
       try { closeDatabase(); } catch { /* */ }
       try { rmSync(base, { recursive: true, force: true }); } catch { /* */ }
@@ -210,6 +235,23 @@ test("advance() logs an engine warning when the uok gate emit fails (orchestrato
   assert.ok(uokFail!.context?.gateId, "the failing gate id must be captured in context");
 });
 
+test("advance() resolves disabled uok gate flags once before gate emission", async (t) => {
+  const f = makeFixture({ dropGateRuns: true, disableUokGates: true });
+  t.after(() => f.cleanup());
+
+  const { logs } = await captureLogs(() => f.orchestrator.advance());
+
+  assert.equal(
+    logs.some((e) => e.component === "engine" && /uok gate emit failed/u.test(e.message)),
+    false,
+    "disabled uok gates must not construct the runner or write gate rows",
+  );
+  assert.ok(
+    f.getAvailableCalls() <= 2,
+    `uok gate preferences should be resolved once per advance, not once per emitted gate (getAvailable calls: ${f.getAvailableCalls()})`,
+  );
+});
+
 // orchestrator.ts:637 — mergePendingCompleteMilestone catches a
 // rebuildMarkdownProjectionsFromDb failure after the system-owned milestone
 // merge and logs `markdown projection rebuild after settlement merge failed`.

package/src/resources/extensions/gsd/tests/orphan-stash-audit.test.ts

@@ -1,6 +1,7 @@
 // gsd-pi + src/resources/extensions/gsd/tests/orphan-stash-audit.test.ts
-// Regression: orphaned gsd-preflight-stash entries from completed milestones
-// must be auto-applied at startup so the user's pre-merge work returns.
+// Regression coverage for orphaned gsd-preflight-stash entries from completed
+// milestones: safe startup recovery for untracked work, manual warnings for
+// tracked or dirty-tree cases that would silently mutate user state.
 
 import { describe, test, beforeEach, afterEach } from "node:test";
 import assert from "node:assert/strict";
@@ -37,6 +38,13 @@ function pushPreflightStash(repo: string, milestoneId: string, fileName: string,
   return marker;
 }
 
+function pushTrackedPreflightStash(repo: string, milestoneId: string, fileName: string, content: string): string {
+  writeFileSync(join(repo, fileName), content);
+  const marker = `gsd-preflight-stash:${milestoneId}:42:1700000000000:tracked`;
+  git(repo, "stash", "push", "-m", `gsd-preflight-stash [${marker}]`);
+  return marker;
+}
+
 describe("auditOrphanedPreflightStashes", () => {
   let repo: string;
 
@@ -83,6 +91,23 @@ describe("auditOrphanedPreflightStashes", () => {
     assert.match(list, /gsd-preflight-stash:M002:/);
   });
 
+  test("does not auto-apply a tracked orphan preflight stash onto a clean working tree", () => {
+    pushTrackedPreflightStash(repo, "M006", "seed.txt", "seed\ntracked pre-merge work\n");
+    assert.equal(readFileSync(join(repo, "seed.txt"), "utf-8"), "seed\n");
+
+    const result = auditOrphanedPreflightStashes(repo, () => true);
+
+    assert.equal(result.applied.length, 0);
+    assert.equal(result.warnings.length, 1);
+    assert.match(result.warnings[0], /not auto-applied/);
+    assert.match(result.warnings[0], /stash modifies tracked files/);
+    assert.match(result.warnings[0], /git stash apply stash@\{\d+\}/);
+    assert.equal(readFileSync(join(repo, "seed.txt"), "utf-8"), "seed\n");
+
+    const list = git(repo, "stash", "list");
+    assert.match(list, /gsd-preflight-stash:M006:/);
+  });
+
   test("ignores stashes whose milestone is not complete", () => {
     pushPreflightStash(repo, "M003", "wip.txt", "still-working\n");
 
@@ -115,23 +140,25 @@ describe("auditOrphanedPreflightStashes", () => {
     assert.match(result.warnings[0], /db unavailable/);
   });
 
-  test("collects a warning when stash apply fails (conflicting working tree)", () => {
-    // Push a stash containing a change to seed.txt; then dirty seed.txt with
-    // a conflicting modification before the audit runs so apply fails.
+  test("collects a warning instead of applying when the working tree is not clean", () => {
+    // Push a stash containing a change to seed.txt; then dirty seed.txt before
+    // the audit runs. Startup recovery must leave the tree untouched and ask
+    // the user to apply the retained backup stash manually.
     writeFileSync(join(repo, "seed.txt"), "stashed\n");
     const marker = `gsd-preflight-stash:M005:42:1700:zz`;
     git(repo, "stash", "push", "-m", `gsd-preflight-stash [${marker}]`);
 
-    // Dirty the working tree so apply will conflict.
     writeFileSync(join(repo, "seed.txt"), "conflicting modification\n");
 
     const result = auditOrphanedPreflightStashes(repo, () => true);
 
     assert.equal(result.applied.length, 0);
     assert.equal(result.warnings.length, 1);
-    assert.match(result.warnings[0], /Could not apply orphaned preflight stash/);
+    assert.match(result.warnings[0], /not auto-applied/);
+    assert.match(result.warnings[0], /working tree not clean/);
     assert.match(result.warnings[0], /M005/);
     assert.match(result.warnings[0], /git stash apply/);
+    assert.equal(readFileSync(join(repo, "seed.txt"), "utf-8"), "conflicting modification\n");
 
     const list = git(repo, "stash", "list");
     assert.match(list, /gsd-preflight-stash:M005:/);
@@ -169,6 +196,63 @@ describe("auditOrphanedPreflightStashes", () => {
       "second run must NOT warn — files are already restored from first run",
     );
   });
+
+  test("warns instead of silently skipping when only some stash untracked files were restored", () => {
+    // Cursor Bugbot caught: isAlreadyRestoredUntrackedStatus treated a dirty
+    // tree as fully restored when every *current* untracked path appeared in
+    // the stash, without requiring every *stash* untracked path to be present.
+    // A partial restore (only some files recovered) was misread as the
+    // idempotent steady state, so the audit no-oped and the remaining pre-merge
+    // files stayed missing with no warning.
+    writeFileSync(join(repo, "first.txt"), "first\n");
+    writeFileSync(join(repo, "second.txt"), "second\n");
+    const marker = `gsd-preflight-stash:M007:42:1700000000000:partial`;
+    git(repo, "stash", "push", "--include-untracked", "-m", `gsd-preflight-stash [${marker}]`);
+
+    // Both files are stashed away.
+    assert.equal(existsSync(join(repo, "first.txt")), false);
+    assert.equal(existsSync(join(repo, "second.txt")), false);
+
+    // Simulate a partial restore: only first.txt came back; second.txt is still
+    // missing from the working tree.
+    writeFileSync(join(repo, "first.txt"), "first\n");
+
+    const result = auditOrphanedPreflightStashes(repo, () => true);
+
+    // Must NOT be treated as already-restored: second.txt is still missing, so
+    // the audit must surface a manual-recovery warning rather than no-op.
+    assert.equal(result.applied.length, 0);
+    assert.equal(result.warnings.length, 1, "partial restore must warn, not silently no-op");
+    assert.match(result.warnings[0], /not auto-applied/);
+    assert.match(result.warnings[0], /working tree not clean/);
+    assert.match(result.warnings[0], /M007/);
+    assert.match(result.warnings[0], /git stash apply/);
+
+    // The stash entry must remain so the user can recover second.txt manually.
+    const list = git(repo, "stash", "list");
+    assert.match(list, /gsd-preflight-stash:M007:/);
+  });
+
+  test("fully restored multi-file untracked stash stays a silent no-op", () => {
+    // Guards the other direction of the set-equality fix: when EVERY stash
+    // untracked file is present in the working tree, the genuine idempotent
+    // steady state must still be recognized and skipped without warning, even
+    // when the stash captured more than one file.
+    writeFileSync(join(repo, "alpha.txt"), "alpha\n");
+    writeFileSync(join(repo, "beta.txt"), "beta\n");
+    const marker = `gsd-preflight-stash:M008:42:1700000000000:multi`;
+    git(repo, "stash", "push", "--include-untracked", "-m", `gsd-preflight-stash [${marker}]`);
+
+    const first = auditOrphanedPreflightStashes(repo, () => true);
+    assert.equal(first.applied.length, 1, "first run applies both files");
+    assert.equal(first.warnings.length, 0);
+    assert.equal(existsSync(join(repo, "alpha.txt")), true);
+    assert.equal(existsSync(join(repo, "beta.txt")), true);
+
+    const second = auditOrphanedPreflightStashes(repo, () => true);
+    assert.equal(second.applied.length, 0, "second run skips");
+    assert.equal(second.warnings.length, 0, "fully restored multi-file stash must not warn");
+  });
 });
 
 test("_isAlreadyRestoredApplyError detects the git stash apply already-exists error", () => {

package/src/resources/extensions/gsd/tests/parallel-research-dispatch.test.ts

@@ -145,6 +145,32 @@ describe("parallel-research-slices dispatch rule", () => {
     }
   });
 
+  test("dispatches parallel research for S01 even when milestone research exists", async () => {
+    writeRoadmap(base, "M001", [
+      { id: "S01", title: "Alpha" },
+      { id: "S02", title: "Beta" },
+    ]);
+    writeFileSync(
+      join(base, ".gsd", "milestones", "M001", "M001-RESEARCH.md"),
+      "# Milestone Research\n",
+      "utf-8",
+    );
+
+    const action = await resolveDispatch({
+      basePath: base,
+      mid: "M001",
+      midTitle: "Parallel Research Milestone",
+      state: baseState(),
+      prefs: undefined,
+    });
+
+    assert.equal(action.action, "dispatch");
+    if (action.action === "dispatch") {
+      assert.equal(action.unitType, "research-slice");
+      assert.equal(action.unitId, "M001/parallel-research");
+    }
+  });
+
   test("does not dispatch parallel research with only one ready slice", async () => {
     writeRoadmap(base, "M001", [{ id: "S01", title: "Alpha" }]);
 

package/src/resources/extensions/gsd/tests/parsers-legacy-importers.test.ts

@@ -54,9 +54,12 @@ const ALLOWED_IMPORTERS = new Set([
   // explicit degraded-mode fallback when DB has no task rows (warns on use)
   "gsd/reactive-graph.ts",
   // recovery path: explicit pre-migration/DB-unavailable fallback branches
-  "gsd/auto-recovery.ts",
+  // (verifyExpectedArtifact extracted here from auto-recovery.ts)
+  "gsd/artifact-verification.ts",
   // diagnostics-only surfaces: report on projections, make no dispatch decisions
   "gsd/doctor.ts",
+  // diagnostics-only: compares PLAN.md task checkboxes against DB status
+  "gsd/doctor-engine-checks.ts",
   // display/telemetry-only surfaces
   "gsd/workspace-index.ts",
   "gsd/visualizer-data.ts",

package/src/resources/extensions/gsd/tests/pipeline-variant-dispatch.test.ts

@@ -22,7 +22,7 @@ import { invalidateAllCaches } from "../cache.ts";
 import type { GSDState } from "../types.ts";
 
 const PARALLEL_RESEARCH_RULE = "planning (multiple slices need research) → parallel-research-slices";
-const SINGLE_RESEARCH_RULE = "planning (no research, not S01) → research-slice";
+const SINGLE_RESEARCH_RULE = "planning (no research) → research-slice";
 const VALIDATE_RULE = "validating-milestone → validate-milestone";
 
 // ─── Fixture helpers ──────────────────────────────────────────────────────

package/src/resources/extensions/gsd/tests/plan-slice-prompt.test.ts

@@ -94,6 +94,16 @@ test("plan-slice prompt: absence checks use negated quiet searches", () => {
   assert.ok(result.includes("count commands exit 1 when they find zero matches"));
 });
 
+test("plan-slice prompt: npm package existence rule is stated during generation", () => {
+  const result = loadPrompt("plan-slice", { ...BASE_VARS, commitInstruction: "Do not commit." });
+  assert.ok(result.includes("reference only packages that exist on the public npm registry"));
+  assert.ok(result.includes("remove or correct any package name that is not real"));
+  // The post-unit pre-execution gate parses package names from require/import
+  // patterns too, not just install commands, so the rule must cover that scope.
+  assert.ok(result.includes("require('...')"));
+  assert.ok(result.includes("import ... from '...'"));
+});
+
 test("plan-slice prompt: footer references gsd_plan_slice tool, not direct write", () => {
   const result = loadPrompt("plan-slice", { ...BASE_VARS, commitInstruction: "Do not commit." });
   assert.ok(

package/src/resources/extensions/gsd/tests/plan-slice.test.ts

@@ -8,6 +8,7 @@ import { tmpdir } from 'node:os';
 
 import { openDatabase, closeDatabase, insertMilestone, insertSlice, insertTask, getSlice, getSliceTasks, getTask, getGateResults, updateTaskStatus } from '../gsd-db.ts';
 import { handlePlanSlice } from '../tools/plan-slice.ts';
+import { handlePlanTask } from '../tools/plan-task.ts';
 import { parsePlan } from '../parsers-legacy.ts';
 import { deriveState, invalidateStateCache } from '../state.ts';
 
@@ -511,15 +512,113 @@ test('handlePlanSlice leaves omitted enrichment fields empty instead of renderin
   }
 });
 
-test('handlePlanSlice rejects invalid payloads', async () => {
+test('handlePlanSlice accepts metadata-only payloads without deleting existing tasks', async () => {
   const base = makeTmpBase();
   openDatabase(join(base, '.gsd', 'gsd.db'));
 
   try {
     seedParentSlice();
-    const result = await handlePlanSlice({ ...validParams(), tasks: [] }, base);
-    assert.ok('error' in result);
-    assert.match(result.error, /validation failed: tasks must be a non-empty array/);
+    const first = await handlePlanSlice(validParams(), base);
+    assert.ok(!('error' in first), `unexpected error: ${'error' in first ? first.error : ''}`);
+    assert.equal(getSliceTasks('M001', 'S02').length, 2);
+
+    const second = await handlePlanSlice({
+      milestoneId: 'M001',
+      sliceId: 'S02',
+      goal: 'Persist updated slice metadata before incremental tasks.',
+      successCriteria: '- Metadata renders before task planning',
+      proofLevel: 'unit',
+      integrationClosure: 'Task details follow through gsd_plan_task.',
+      observabilityImpact: 'Progress survives between tool calls.',
+    }, base);
+    assert.ok(!('error' in second), `unexpected error: ${'error' in second ? second.error : ''}`);
+    assert.equal(getSlice('M001', 'S02')?.goal, 'Persist updated slice metadata before incremental tasks.');
+    assert.deepEqual(getSliceTasks('M001', 'S02').map((task) => task.id), ['T01', 'T02']);
+
+    const third = await handlePlanSlice({ ...validParams(), tasks: [] }, base);
+    assert.ok(!('error' in third), `unexpected error: ${'error' in third ? third.error : ''}`);
+    assert.deepEqual(getSliceTasks('M001', 'S02').map((task) => task.id), ['T01', 'T02']);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test('handlePlanSlice metadata-only on a fresh sketch slice keeps is_sketch set and renders no PLAN.md (#1027)', async () => {
+  const base = makeTmpBase();
+  openDatabase(join(base, '.gsd', 'gsd.db'));
+
+  try {
+    insertMilestone({ id: 'M001', title: 'Milestone', status: 'active' });
+    insertSlice({ id: 'S02', milestoneId: 'M001', title: 'Planning slice', status: 'pending', demo: 'Rendered plans exist.', isSketch: true });
+
+    // The incremental flow's first call carries metadata only (no tasks). It
+    // must NOT error (renderPlanFromDb throws on a task-less slice), and it must
+    // NOT clear the sketch flag — clearing it without a PLAN.md would leave the
+    // slice out of refining with no plan artifact, breaking sketch/plan signaling.
+    const result = await handlePlanSlice({
+      milestoneId: 'M001',
+      sliceId: 'S02',
+      goal: 'Persist slice metadata before any tasks exist.',
+    }, base);
+    assert.ok(!('error' in result), `unexpected error: ${'error' in result ? result.error : ''}`);
+    assert.equal(getSlice('M001', 'S02')?.goal, 'Persist slice metadata before any tasks exist.');
+    assert.equal(getSliceTasks('M001', 'S02').length, 0);
+    assert.equal(getSlice('M001', 'S02')?.is_sketch, 1, 'sketch flag must stay set until a task-bearing plan renders');
+
+    const planPath = join(base, '.gsd', 'phases', '01-test', '01-02-PLAN.md');
+    assert.ok(!existsSync(planPath), 'no PLAN.md should be rendered until the first task is planned');
+
+    invalidateStateCache();
+    const after = await deriveState(base);
+    assert.equal(after.phase, 'refining', 'a task-less sketch slice stays in refining');
+  } finally {
+    cleanup(base);
+  }
+});
+
+test('handlePlanTask materializes the slice PLAN.md and clears the sketch flag on the incremental path (#1027)', async () => {
+  const base = makeTmpBase();
+  openDatabase(join(base, '.gsd', 'gsd.db'));
+
+  try {
+    insertMilestone({ id: 'M001', title: 'Milestone', status: 'active' });
+    insertSlice({ id: 'S02', milestoneId: 'M001', title: 'Planning slice', status: 'pending', demo: 'Rendered plans exist.', isSketch: true });
+
+    const sliceResult = await handlePlanSlice({
+      milestoneId: 'M001',
+      sliceId: 'S02',
+      goal: 'Incrementally planned slice.',
+      successCriteria: '- The slice plan is built up one task at a time',
+    }, base);
+    assert.ok(!('error' in sliceResult), `unexpected error: ${'error' in sliceResult ? sliceResult.error : ''}`);
+
+    const taskResult = await handlePlanTask({
+      milestoneId: 'M001',
+      sliceId: 'S02',
+      taskId: 'T01',
+      title: 'First incremental task',
+      description: 'Implement the first task added through gsd_plan_task.',
+      estimate: '30m',
+      files: ['src/resources/extensions/gsd/tools/plan-task.ts'],
+      verify: 'node --test src/resources/extensions/gsd/tests/plan-task.test.ts',
+      inputs: ['src/resources/extensions/gsd/tools/plan-milestone.ts'],
+      expectedOutput: ['src/resources/extensions/gsd/tools/plan-task.ts'],
+    }, base);
+    assert.ok(!('error' in taskResult), `unexpected error: ${'error' in taskResult ? taskResult.error : ''}`);
+
+    // The first incremental task materializes the canonical slice PLAN.md with
+    // the task present, and clears the sketch flag now that a plan exists.
+    const planPath = join(base, '.gsd', 'phases', '01-test', '01-02-PLAN.md');
+    assert.ok(existsSync(planPath), 'slice PLAN.md should exist after the first task is planned');
+    const parsedPlan = parsePlan(readFileSync(planPath, 'utf-8'));
+    assert.equal(parsedPlan.goal, 'Incrementally planned slice.');
+    assert.equal(parsedPlan.tasks.length, 1);
+    assert.equal(parsedPlan.tasks[0]?.id, 'T01');
+    assert.equal(getSlice('M001', 'S02')?.is_sketch, 0, 'sketch flag must clear once the first task renders a plan');
+
+    invalidateStateCache();
+    const after = await deriveState(base);
+    assert.notEqual(after.phase, 'refining', 'a planned slice leaves refining');
   } finally {
     cleanup(base);
   }

package/src/resources/extensions/gsd/tests/plan-task.test.ts

@@ -4,7 +4,7 @@ import { mkdtempSync, mkdirSync, rmSync, readFileSync, existsSync, writeFileSync
 import { join } from 'node:path';
 import { tmpdir } from 'node:os';
 
-import { openDatabase, closeDatabase, insertMilestone, insertSlice, insertTask, getTask } from '../gsd-db.ts';
+import { openDatabase, closeDatabase, insertMilestone, insertSlice, insertTask, getSlice, getTask, getGateResults } from '../gsd-db.ts';
 import { handlePlanTask } from '../tools/plan-task.ts';
 import { parseTaskPlanFile } from '../files.ts';
 
@@ -65,6 +65,25 @@ test('handlePlanTask writes planning state and renders task plan', async () => {
   }
 });
 
+test('handlePlanTask seeds execute-task gate rows for incremental planning', async () => {
+  const base = makeTmpBase();
+  openDatabase(join(base, '.gsd', 'gsd.db'));
+
+  try {
+    seedParent();
+    const result = await handlePlanTask(validParams(), base);
+    assert.ok(!('error' in result), `unexpected error: ${'error' in result ? result.error : ''}`);
+
+    const gateIds = getGateResults('M001', 'S02', 'task')
+      .filter((gate) => gate.task_id === 'T02')
+      .map((gate) => gate.gate_id)
+      .sort();
+    assert.deepEqual(gateIds, ['Q5', 'Q6', 'Q7']);
+  } finally {
+    cleanup(base);
+  }
+});
+
 test('handlePlanTask rejects invalid payloads', async () => {
   const base = makeTmpBase();
   openDatabase(join(base, '.gsd', 'gsd.db'));
@@ -170,6 +189,30 @@ test('handlePlanTask surfaces render failures without changing parse-visible tas
   }
 });
 
+test('handlePlanTask keeps the sketch flag set when the flat-phase slice plan sync fails (#1083)', async () => {
+  const base = makeTmpBase();
+  openDatabase(join(base, '.gsd', 'gsd.db'));
+
+  try {
+    insertMilestone({ id: 'M001', title: 'Milestone', status: 'active' });
+    insertSlice({ id: 'S02', milestoneId: 'M001', title: 'Planning slice', status: 'pending', demo: 'Rendered plans exist.', isSketch: true });
+
+    // The per-task render writes T02-PLAN.md and succeeds, but the flat-phase
+    // slice re-render (the canonical PLAN.md that embeds task checkboxes) targets
+    // phases/01-test/01-02-PLAN.md. Pre-creating that path as a directory forces
+    // EISDIR on the slice sync, so the canonical slice plan never reflects the
+    // task. The sketch flag must therefore stay set — the slice keeps refining —
+    // instead of leaving the slice out of refining over a stale plan.
+    mkdirSync(join(base, '.gsd', 'phases', '01-test', '01-02-PLAN.md'), { recursive: true });
+
+    const result = await handlePlanTask(validParams(), base);
+    assert.equal(getSlice('M001', 'S02')?.is_sketch, 1, 'sketch flag must stay set when the canonical slice plan could not sync');
+    assert.ok(getTask('M001', 'S02', 'T02'), 'the task itself is still persisted so the slice can re-sync on retry');
+  } finally {
+    cleanup(base);
+  }
+});
+
 test('handlePlanTask reruns idempotently and refreshes parse-visible state', async () => {
   const base = makeTmpBase();
   openDatabase(join(base, '.gsd', 'gsd.db'));

package/src/resources/extensions/gsd/tests/post-mutation-hook.test.ts

@@ -10,7 +10,7 @@ import * as os from 'node:os';
 import { openDatabase, closeDatabase } from '../gsd-db.ts';
 import { handleCompleteTask } from '../tools/complete-task.ts';
 import { readEvents } from '../workflow-events.ts';
-import { readManifest } from '../workflow-manifest.ts';
+import { flushManifest, readManifest } from '../workflow-manifest.ts';
 
 function tempDir(): string {
   return fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-post-hook-'));
@@ -115,8 +115,9 @@ test('post-mutation-hook: state-manifest.json exists after handleCompleteTask',
     const result = await handleCompleteTask(makeCompleteTaskParams(), base);
     assert.ok(!('error' in result), `handler should succeed, got: ${JSON.stringify(result)}`);
 
+    await flushManifest(base);
     const manifestPath = path.join(base, '.gsd', 'state-manifest.json');
-    assert.ok(fs.existsSync(manifestPath), 'state-manifest.json should exist after handler completes');
+    assert.ok(fs.existsSync(manifestPath), 'state-manifest.json should exist after manifest flush');
   } finally {
     closeDatabase();
     cleanupDir(base);
@@ -131,6 +132,7 @@ test('post-mutation-hook: manifest has version 1 and includes completed task', a
 
   try {
     await handleCompleteTask(makeCompleteTaskParams(), base);
+    await flushManifest(base);
 
     const manifest = readManifest(base);
     assert.ok(manifest !== null, 'manifest should be readable');

package/src/resources/extensions/gsd/tests/prefs-wizard-coverage.test.ts

@@ -6,7 +6,12 @@ import { mkdtempSync, readFileSync, rmSync } from "node:fs";
 import { join } from "node:path";
 import { tmpdir } from "node:os";
 
-import { buildCategorySummaries, handlePrefsWizard } from "../commands-prefs-wizard.ts";
+import {
+  buildCategorySummaries,
+  handlePrefsWizard,
+  serializePreferencesToFrontmatter,
+} from "../commands-prefs-wizard.ts";
+import { parsePreferencesMarkdown, validatePreferences } from "../preferences.ts";
 import { KNOWN_PREFERENCE_KEYS } from "../preferences-types.ts";
 
 const PREF_SAMPLE_VALUES: Record<string, unknown> = {
@@ -103,6 +108,54 @@ const PREF_SAMPLE_VALUES: Record<string, unknown> = {
   },
 };
 
+test("prefs serializer preserves nested hook on_block objects", () => {
+  const frontmatter = serializePreferencesToFrontmatter({
+    post_unit_hooks: [{
+      name: "plan-review",
+      after: ["execute-task"],
+      prompt: "write PLAN-REVIEW.md",
+      artifact: "PLAN-REVIEW.md",
+      criticality: "blocking",
+      on_block: { action: "pause" },
+    }],
+  });
+
+  assert.doesNotMatch(frontmatter, /\[object Object\]/);
+  assert.ok(frontmatter.includes("    on_block:\n      action: pause\n"));
+
+  const parsed = parsePreferencesMarkdown(`---\n${frontmatter}---\n`);
+  assert.notEqual(parsed, null);
+
+  const { errors, preferences } = validatePreferences(parsed!);
+  assert.deepEqual(errors, []);
+  assert.deepEqual(preferences.post_unit_hooks?.[0]?.on_block, { action: "pause" });
+});
+
+test("prefs serializer correctly indents nested object when it is the first array-item property", () => {
+  // on_block is the FIRST property — exercises the first-key-is-object branch
+  const frontmatter = serializePreferencesToFrontmatter({
+    post_unit_hooks: [{
+      on_block: { action: "pause" }, // first property — exercises the first-key-is-object branch
+      name: "gate",                  // required fields come after so on_block stays first
+      after: ["execute-task"],
+      prompt: "review output",
+    }],
+  });
+
+  assert.doesNotMatch(frontmatter, /\[object Object\]/);
+  // Children of on_block must be indented deeper than on_block itself (not siblings)
+  assert.ok(
+    frontmatter.includes("  - on_block:\n      action: pause\n"),
+    `Expected on_block children indented as nested YAML, got:\n${frontmatter}`,
+  );
+  // Sanity: parse + validate round-trip
+  const parsed = parsePreferencesMarkdown(`---\n${frontmatter}---\n`);
+  assert.notEqual(parsed, null);
+  const { errors, preferences } = validatePreferences(parsed!);
+  assert.deepEqual(errors, []);
+  assert.deepEqual(preferences.post_unit_hooks?.[0]?.on_block, { action: "pause" });
+});
+
 test("prefs wizard save path preserves every known preference key", async () => {
   const missingSamples = [...KNOWN_PREFERENCE_KEYS].filter((key) => !(key in PREF_SAMPLE_VALUES));
   assert.deepEqual(missingSamples, [], "test fixture must cover every known preference key");