@opengsd/gsd-pi 1.4.0 → 1.5.0

package/src/resources/extensions/gsd/tests/auto-timeout-recovery-harness-abort.test.ts

@@ -0,0 +1,55 @@
+import test from "node:test";
+import assert from "node:assert/strict";
+import { mkdtempSync, mkdirSync, rmSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+
+import { recoverTimedOutUnit } from "../auto-timeout-recovery.ts";
+import {
+  readUnitHarnessAbort,
+  readUnitRuntimeRecord,
+  recordUnitHarnessAbort,
+} from "../unit-runtime.ts";
+
+test("timeout recovery retry clears stale harness abort for the same unit run", async () => {
+  const base = mkdtempSync(join(tmpdir(), "gsd-timeout-recovery-abort-"));
+  const startedAt = Date.now();
+  mkdirSync(join(base, ".gsd"), { recursive: true });
+  try {
+    recordUnitHarnessAbort(base, "gate-evaluate", "M001/S01/gates+Q3", startedAt, {
+      kind: "turn-abort",
+      reason: "Agent turn aborted before the unit could complete its gate evaluation.",
+    });
+    assert.equal(
+      readUnitHarnessAbort(base, "gate-evaluate", "M001/S01/gates+Q3", startedAt)?.kind,
+      "turn-abort",
+      "test setup should start with an abort marker",
+    );
+
+    const messages: Array<{ message: unknown; options: unknown }> = [];
+    const notifications: Array<{ message: string; level?: string }> = [];
+    const result = await recoverTimedOutUnit(
+      { ui: { notify: (message: string, level?: string) => notifications.push({ message, level }) } } as any,
+      { sendMessage: (message: unknown, options: unknown) => messages.push({ message, options }) } as any,
+      "gate-evaluate",
+      "M001/S01/gates+Q3",
+      "idle",
+      {
+        basePath: base,
+        verbose: false,
+        currentUnitStartedAt: startedAt,
+        unitRecoveryCount: new Map(),
+      },
+    );
+
+    assert.equal(result, "recovered");
+    assert.equal(readUnitHarnessAbort(base, "gate-evaluate", "M001/S01/gates+Q3", startedAt), null);
+    const record = readUnitRuntimeRecord(base, "gate-evaluate", "M001/S01/gates+Q3");
+    assert.equal(record?.phase, "recovered");
+    assert.equal(record?.lastProgressKind, "idle-recovery-retry");
+    assert.equal(messages.length, 1, "retry recovery should send one steering message");
+    assert.equal(notifications.length, 1, "retry recovery should notify once");
+  } finally {
+    rmSync(base, { recursive: true, force: true });
+  }
+});

package/src/resources/extensions/gsd/tests/auto-warning-noise-regression.test.ts

@@ -34,6 +34,11 @@ import {
   clearPendingAutoStart,
   setPendingAutoStart,
 } from "../guided-flow.ts";
+import {
+  closeDatabase,
+  insertMilestone,
+  openDatabase,
+} from "../gsd-db.ts";
 
 // ─── Bug 2: this-binding regression ─────────────────────────────────────
 
@@ -89,6 +94,8 @@ test("checkAutoStartAfterDiscuss completes when discussion manifest is absent",
     mkdirSync(milestoneDir, { recursive: true });
     writeFileSync(join(milestoneDir, "M001-CONTEXT.md"), "# Context\n", "utf-8");
     writeFileSync(join(base, ".gsd", "STATE.md"), "# State\n", "utf-8");
+    openDatabase(":memory:");
+    insertMilestone({ id: "M001", title: "M001", status: "queued" });
     setPendingAutoStart(base, {
       basePath: base,
       milestoneId: "M001",
@@ -110,6 +117,7 @@ test("checkAutoStartAfterDiscuss completes when discussion manifest is absent",
       },
     ]);
   } finally {
+    closeDatabase();
     clearPendingAutoStart(base);
     rmSync(base, { recursive: true, force: true });
   }

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

@@ -0,0 +1,85 @@
+// batch-task-query.test.ts
+// Verifies getTasksBySliceIds batches tasks correctly and matches the per-slice
+// getSliceTasks path (guards the projection N+1 fix).
+
+import { test } from "node:test";
+import assert from "node:assert/strict";
+import { mkdtempSync, mkdirSync, rmSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+
+import {
+  openDatabase,
+  closeDatabase,
+  insertMilestone,
+  insertSlice,
+  insertTask,
+  getSliceTasks,
+  getTasksBySliceIds,
+} from "../gsd-db.ts";
+
+function withDb(fn: () => void): void {
+  const base = mkdtempSync(join(tmpdir(), "gsd-batch-task-"));
+  mkdirSync(join(base, ".gsd"), { recursive: true });
+  try {
+    openDatabase(join(base, ".gsd", "gsd.db"));
+    fn();
+  } finally {
+    try { closeDatabase(); } catch {}
+    try { rmSync(base, { recursive: true, force: true }); } catch {}
+  }
+}
+
+function seed(): void {
+  insertMilestone({ id: "M001", title: "M1", status: "active" });
+  insertMilestone({ id: "M002", title: "M2", status: "active" });
+  insertSlice({ id: "S01", milestoneId: "M001", title: "S1", status: "active", risk: "low", depends: [] });
+  insertSlice({ id: "S02", milestoneId: "M001", title: "S2", status: "pending", risk: "low", depends: [] });
+  insertSlice({ id: "S01", milestoneId: "M002", title: "S1", status: "active", risk: "low", depends: [] });
+  // M001/S01 has two tasks; M001/S02 has one; M002/S01 has none.
+  insertTask({ id: "T02", sliceId: "S01", milestoneId: "M001", title: "second", status: "pending" });
+  insertTask({ id: "T01", sliceId: "S01", milestoneId: "M001", title: "first", status: "complete" });
+  insertTask({ id: "T01", sliceId: "S02", milestoneId: "M001", title: "only", status: "pending" });
+}
+
+const key = (m: string, s: string) => `${m}\0${s}`;
+
+test("getTasksBySliceIds buckets tasks per (milestone, slice)", () => {
+  withDb(() => {
+    seed();
+    const map = getTasksBySliceIds([
+      { milestoneId: "M001", sliceId: "S01" },
+      { milestoneId: "M001", sliceId: "S02" },
+      { milestoneId: "M002", sliceId: "S01" },
+    ]);
+    assert.equal(map.get(key("M001", "S01"))?.length, 2);
+    assert.equal(map.get(key("M001", "S02"))?.length, 1);
+    // A slice with no tasks is absent (caller falls back to []).
+    assert.equal(map.has(key("M002", "S01")), false);
+  });
+});
+
+test("getTasksBySliceIds preserves ORDER BY sequence, id within a bucket", () => {
+  withDb(() => {
+    seed();
+    const bucket = getTasksBySliceIds([{ milestoneId: "M001", sliceId: "S01" }]).get(key("M001", "S01"));
+    // Insertion order was T02 then T01; ordering is by sequence then id, so T01 first.
+    assert.deepEqual(bucket?.map((t) => t.id), ["T01", "T02"]);
+  });
+});
+
+test("getTasksBySliceIds equals getSliceTasks for a single slice", () => {
+  withDb(() => {
+    seed();
+    const batched = getTasksBySliceIds([{ milestoneId: "M001", sliceId: "S01" }]).get(key("M001", "S01"));
+    const direct = getSliceTasks("M001", "S01");
+    assert.deepEqual(batched, direct);
+  });
+});
+
+test("getTasksBySliceIds returns an empty map for empty input", () => {
+  withDb(() => {
+    seed();
+    assert.equal(getTasksBySliceIds([]).size, 0);
+  });
+});

package/src/resources/extensions/gsd/tests/check-auto-start-ready-guard.test.ts

@@ -13,6 +13,7 @@ import {
   checkAutoStartAfterDiscuss,
   setPendingAutoStart,
   clearPendingAutoStart,
+  _getPendingAutoStart,
 } from "../guided-flow.ts";
 import { drainLogs } from "../workflow-logger.ts";
 import {
@@ -77,6 +78,7 @@ describe("checkAutoStartAfterDiscuss ready-notify DB guard (R3b)", () => {
   let cap: MockCapture;
 
   beforeEach(() => {
+    closeDatabase();
     clearPendingAutoStart();
     drainLogs();
   });
@@ -129,6 +131,33 @@ describe("checkAutoStartAfterDiscuss ready-notify DB guard (R3b)", () => {
     ]);
   });
 
+  test("fails closed and keeps pending handoff when DB is unavailable", () => {
+    base = mkBase();
+    closeDatabase();
+
+    cap = mkCapture();
+    setPendingAutoStart(base, {
+      basePath: base,
+      milestoneId: "M001",
+      startAuto: false,
+      ctx: mkCtx(cap),
+      pi: mkPi(cap),
+    });
+
+    const result = checkAutoStartAfterDiscuss();
+    assert.equal(result, false, "DB-unavailable handoff must fail closed");
+    assert.equal(
+      _getPendingAutoStart(base)?.milestoneId,
+      "M001",
+      "failed closed handoff must remain pending for a later retry",
+    );
+    assert.equal(
+      cap.notifies.some(n => n.level === "success"),
+      false,
+      "must not notify success before the milestone row is verified",
+    );
+  });
+
   test("announces 'ready' when DB row has executable slices", () => {
     base = mkBase();
     openDatabase(":memory:");

package/src/resources/extensions/gsd/tests/codebase-generator.test.ts

@@ -722,3 +722,368 @@ test("ensureCodebaseMapFresh: uses TTL cache before enumerating files", () => {
     cleanup(base);
   }
 });
+
+// ─── Workspace-aware (parent mode) ───────────────────────────────────────
+
+/**
+ * Build a parent workspace: a parent git repo whose .gsd/PREFERENCES.md declares
+ * child repositories, each child being its own separate git repo nested inside.
+ */
+function makeTmpParentWorkspace(children: string[]): string {
+  const base = join(tmpdir(), `gsd-codebase-parent-${randomUUID()}`);
+  mkdirSync(join(base, ".gsd"), { recursive: true });
+  execSync("git init", { cwd: base, stdio: "ignore" });
+
+  const repoLines = children.map((id) => `    ${id}:\n      path: ${id}`).join("\n");
+  writeFileSync(
+    join(base, ".gsd", "PREFERENCES.md"),
+    `---\nversion: 1\nworkspace:\n  mode: parent\n  repositories:\n${repoLines}\n---\n`,
+    "utf-8",
+  );
+
+  for (const child of children) {
+    const childPath = join(base, child);
+    mkdirSync(childPath, { recursive: true });
+    execSync("git init", { cwd: childPath, stdio: "ignore" });
+  }
+  return base;
+}
+
+function addChildFile(base: string, child: string, path: string, content = ""): void {
+  const childRoot = join(base, child);
+  const fullPath = join(childRoot, path);
+  mkdirSync(join(fullPath, ".."), { recursive: true });
+  writeFileSync(fullPath, content || `// ${child}/${path}\n`, "utf-8");
+  execSync(`git add "${path}"`, { cwd: childRoot, stdio: "ignore" });
+}
+
+test("workspace-aware: parent mode enumerates each declared child repo under a repo heading", () => {
+  const base = makeTmpParentWorkspace(["frontend", "backend"]);
+  try {
+    addChildFile(base, "frontend", "src/App.tsx");
+    addChildFile(base, "backend", "src/server.ts");
+
+    const result = generateCodebaseMap(base);
+
+    // Both repos appear as labelled sections.
+    assert.match(result.content, /## \[frontend\]/);
+    assert.match(result.content, /## \[backend\]/);
+    // Child files are rewritten to workspace-relative paths.
+    assert.match(result.content, /`frontend\/src\/App\.tsx`/);
+    assert.match(result.content, /`backend\/src\/server\.ts`/);
+    assert.equal(result.fileCount, 2);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: metadata records the repositories whose files appear in the map", () => {
+  const base = makeTmpParentWorkspace(["frontend", "backend"]);
+  try {
+    addChildFile(base, "frontend", "src/App.tsx");
+    addChildFile(base, "backend", "src/server.ts");
+
+    const result = generateCodebaseMap(base);
+    const metadata = parseCodebaseMapMetadata(result.content);
+
+    assert.ok(metadata, "metadata should be present");
+    assert.deepEqual(metadata?.repositories?.sort(), ["backend", "frontend"]);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: parseCodebaseMap recovers descriptions across repo sections", () => {
+  const base = makeTmpParentWorkspace(["frontend", "backend"]);
+  try {
+    addChildFile(base, "frontend", "src/App.tsx");
+    addChildFile(base, "backend", "src/server.ts");
+
+    // Seed descriptions keyed by the workspace-relative paths.
+    const descriptions = new Map<string, string>([
+      ["frontend/src/App.tsx", "React entry"],
+      ["backend/src/server.ts", "Express API"],
+    ]);
+    const result = generateCodebaseMap(base, undefined, descriptions);
+    writeCodebaseMap(base, result.content);
+
+    const parsed = parseCodebaseMap(readCodebaseMap(base)!);
+    assert.equal(parsed.get("frontend/src/App.tsx"), "React entry");
+    assert.equal(parsed.get("backend/src/server.ts"), "Express API");
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: project mode (no declared children) stays single-section", () => {
+  // A plain single repo with no workspace config must render exactly as before.
+  const base = makeTmpRepo();
+  try {
+    addFile(base, "src/main.ts");
+
+    const result = generateCodebaseMap(base);
+
+    assert.doesNotMatch(result.content, /## \[/);
+    assert.match(result.content, /`src\/main\.ts`/);
+    const metadata = parseCodebaseMapMetadata(result.content);
+    assert.equal(metadata?.repositories, undefined);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: updateCodebaseMap tracks child-repo file additions", () => {
+  const base = makeTmpParentWorkspace(["frontend"]);
+  try {
+    addChildFile(base, "frontend", "src/App.tsx");
+    const first = updateCodebaseMap(base);
+    writeCodebaseMap(base, first.content);
+    assert.equal(first.added, 1);
+
+    addChildFile(base, "frontend", "src/index.tsx");
+    const second = updateCodebaseMap(base);
+    assert.equal(second.added, 1);
+    assert.equal(second.removed, 0);
+    assert.equal(second.fileCount, 2);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: workspace-relative exclude patterns filter child-repo files", () => {
+  // Regression guard: exclude patterns like `frontend/` are workspace-relative,
+  // so they must be matched against the rewritten path, not the child-relative one.
+  const base = makeTmpParentWorkspace(["frontend", "backend"]);
+  try {
+    addChildFile(base, "frontend", "src/App.tsx");
+    addChildFile(base, "backend", "src/server.ts");
+
+    const result = generateCodebaseMap(base, { excludePatterns: ["frontend/"] });
+
+    assert.doesNotMatch(result.content, /frontend\/src\/App\.tsx/);
+    assert.match(result.content, /backend\/src\/server\.ts/);
+    assert.equal(result.fileCount, 1);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: maxFiles cap does not starve child repos for the project repo", () => {
+  // The implicit project repo is enumerated alongside children; the cap must be
+  // applied fairly (round-robin) so a large project repo cannot crowd out children.
+  const base = makeTmpParentWorkspace(["frontend", "backend"]);
+  try {
+    addChildFile(base, "frontend", "a.ts");
+    addChildFile(base, "frontend", "b.ts");
+    addChildFile(base, "backend", "c.ts");
+
+    // Cap at 2 files — with fair distribution both repos should appear.
+    const result = generateCodebaseMap(base, { maxFiles: 2 });
+    const repoSections = (result.content.match(/^## \[.+\]/gm) ?? []).length;
+
+    assert.equal(result.fileCount, 2);
+    assert.ok(repoSections >= 2, "both child repos should be represented under a tight cap");
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: overlapping paths dedupe without falsely reporting truncation", () => {
+  // Regression guard: a path tracked by both the implicit project repo and a child
+  // repo collapses to one workspace-relative entry. Deduplicated duplicates must not
+  // count toward the maxFiles cap, so the map must not be flagged as truncated.
+  const base = join(tmpdir(), `gsd-codebase-parent-${randomUUID()}`);
+  mkdirSync(join(base, ".gsd"), { recursive: true });
+  execSync("git init", { cwd: base, stdio: "ignore" });
+  writeFileSync(
+    join(base, ".gsd", "PREFERENCES.md"),
+    `---\nversion: 1\nworkspace:\n  mode: parent\n  repositories:\n    lib:\n      path: lib\n---\n`,
+    "utf-8",
+  );
+  try {
+    // The project repo tracks lib/util.ts before lib becomes its own repo; the child
+    // repo then tracks util.ts, so both resolve to the same workspace path lib/util.ts.
+    addFile(base, "lib/util.ts");
+    execSync("git init", { cwd: join(base, "lib"), stdio: "ignore" });
+    execSync("git add util.ts", { cwd: join(base, "lib"), stdio: "ignore" });
+
+    const result = generateCodebaseMap(base);
+
+    assert.equal(result.fileCount, 1);
+    assert.equal(result.truncated, false);
+    assert.equal((result.content.match(/`lib\/util\.ts`/g) ?? []).length, 1);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: project directories interleaving child prefixes stay under one heading", () => {
+  // Regression guard: the implicit project repo has an empty prefix, so its
+  // root-level dirs (aaa/, zzz/) sort lexically around a child prefix (mmm/).
+  // Groups must be ordered per repo so `## [project]` is emitted exactly once.
+  const base = makeTmpParentWorkspace(["mmm"]);
+  try {
+    addFile(base, "aaa/x.ts"); // project repo, sorts before "mmm"
+    addFile(base, "zzz/y.ts"); // project repo, sorts after "mmm"
+    addChildFile(base, "mmm", "src/thing.ts");
+
+    const result = generateCodebaseMap(base);
+
+    const projectHeadings = (result.content.match(/^## \[project\]$/gm) ?? []).length;
+    const mmmHeadings = (result.content.match(/^## \[mmm\]$/gm) ?? []).length;
+    const allHeadings = (result.content.match(/^## \[.+\]$/gm) ?? []).length;
+
+    assert.equal(projectHeadings, 1, "project section must not be split across headings");
+    assert.equal(mmmHeadings, 1);
+    assert.equal(allHeadings, 2);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: renaming a declared repo id invalidates map freshness", () => {
+  // Regression guard: repo identity is rendered into the map, so renaming a repo id
+  // (path unchanged → identical file paths) must be caught by the freshness
+  // fingerprint rather than leaving a stale `## [old-id]` heading in place.
+  const base = makeTmpParentWorkspace(["frontend"]);
+  try {
+    addChildFile(base, "frontend", "src/App.tsx");
+
+    ensureCodebaseMapFresh(base, undefined, { ttlMs: 0, force: true });
+    assert.match(readCodebaseMap(base)!, /^## \[frontend\]$/m);
+
+    // Rename the repo id to `web`; the path (and therefore the file paths) is unchanged.
+    writeFileSync(
+      join(base, ".gsd", "PREFERENCES.md"),
+      `---\nversion: 1\nworkspace:\n  mode: parent\n  repositories:\n    web:\n      path: frontend\n---\n`,
+      "utf-8",
+    );
+
+    const refreshed = ensureCodebaseMapFresh(base, undefined, { ttlMs: 0, force: true });
+    const written = readCodebaseMap(base)!;
+
+    assert.equal(refreshed.status, "updated");
+    assert.match(written, /^## \[web\]$/m);
+    assert.doesNotMatch(written, /^## \[frontend\]$/m);
+    assert.deepEqual(parseCodebaseMapMetadata(written)?.repositories, ["web"]);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("single-repo: directory order stays byte-identical code-unit sort (not locale-aware)", () => {
+  // Byte-identical single-repo invariant: pre-workspace output ordered
+  // directories with a bare `.sort()` (UTF-16 code-unit order), so uppercase
+  // sorts before lowercase ("Zoo" < "apple"). A locale-aware comparator inverts
+  // these and silently changes project-mode CODEBASE.md, so guard the ordering.
+  const base = makeTmpRepo();
+  try {
+    addFile(base, "Zoo/keeper.ts"); // 'Z' (0x5A) < 'a' (0x61) → sorts first
+    addFile(base, "apple/tree.ts");
+
+    const content = generateCodebaseMap(base).content;
+    const zooIdx = content.indexOf("### Zoo/");
+    const appleIdx = content.indexOf("### apple/");
+
+    assert.notEqual(zooIdx, -1);
+    assert.notEqual(appleIdx, -1);
+    assert.ok(zooIdx < appleIdx, "code-unit order must place Zoo/ before apple/");
+    // Project mode emits no repo partition heading.
+    assert.doesNotMatch(content, /^## \[.+\]$/m);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: an invalid workspace registry surfaces an error instead of silently falling back", () => {
+  // Regression guard: a broken parent-mode config (here a child path escaping the
+  // project root) must propagate as an error. Swallowing it and falling back to a
+  // single-root map would silently drop every child repo from planning context.
+  const base = makeTmpRepo();
+  try {
+    addFile(base, "src/main.ts");
+    writeFileSync(
+      join(base, ".gsd", "PREFERENCES.md"),
+      `---\nversion: 1\nworkspace:\n  mode: parent\n  repositories:\n    frontend:\n      path: ../escapes-root\n---\n`,
+      "utf-8",
+    );
+
+    assert.throws(() => generateCodebaseMap(base), /resolves outside project root/);
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("workspace-aware: files sharing a directory across repos keep their own repo heading", () => {
+  // Regression guard: the implicit project repo and a child repo can own different
+  // files under the same workspace-relative directory (lib/). Groups are keyed by
+  // (repo, dir), so each file must render under its own `## [repo-id]` heading
+  // instead of collapsing into one section labelled with a single (wrong) repo.
+  const base = join(tmpdir(), `gsd-codebase-parent-${randomUUID()}`);
+  mkdirSync(join(base, ".gsd"), { recursive: true });
+  execSync("git init", { cwd: base, stdio: "ignore" });
+  writeFileSync(
+    join(base, ".gsd", "PREFERENCES.md"),
+    `---\nversion: 1\nworkspace:\n  mode: parent\n  repositories:\n    lib:\n      path: lib\n---\n`,
+    "utf-8",
+  );
+  try {
+    // Project repo tracks lib/app.ts before lib becomes its own repo; the child
+    // repo then tracks helper.ts → workspace path lib/helper.ts. Different files,
+    // same directory, different repos.
+    addFile(base, "lib/app.ts");
+    execSync("git init", { cwd: join(base, "lib"), stdio: "ignore" });
+    writeFileSync(join(base, "lib", "helper.ts"), "// helper\n", "utf-8");
+    execSync("git add helper.ts", { cwd: join(base, "lib"), stdio: "ignore" });
+
+    const content = generateCodebaseMap(base).content;
+
+    // Both files present, each under its own repo section (not merged under one).
+    assert.match(content, /## \[project\]/);
+    assert.match(content, /## \[lib\]/);
+    const projectIdx = content.indexOf("## [project]");
+    const appIdx = content.indexOf("`lib/app.ts`");
+    const libIdx = content.indexOf("## [lib]");
+    const helperIdx = content.indexOf("`lib/helper.ts`");
+    assert.ok(
+      projectIdx < appIdx && appIdx < libIdx && libIdx < helperIdx,
+      "lib/app.ts must sit under [project] and lib/helper.ts under [lib]",
+    );
+  } finally {
+    cleanup(base);
+  }
+});
+
+test("ensureCodebaseMapFresh: editing declared repos within the TTL window bypasses the cache", () => {
+  // Regression guard: the freshness TTL cache key folds in the workspace signature
+  // (mode + declared repos). Adding a child repo must miss the cache and re-enumerate
+  // rather than serve a stale map that omits the new repo until the TTL expires.
+  const base = makeTmpParentWorkspace(["frontend"]);
+  try {
+    addChildFile(base, "frontend", "src/App.tsx");
+
+    const initial = ensureCodebaseMapFresh(base, undefined, { ttlMs: 60_000 });
+    assert.equal(initial.status, "generated");
+    assert.doesNotMatch(readCodebaseMap(base)!, /## \[backend\]/);
+
+    // Declare a second child repo and back it with a real nested repo + file.
+    mkdirSync(join(base, "backend"), { recursive: true });
+    execSync("git init", { cwd: join(base, "backend"), stdio: "ignore" });
+    addChildFile(base, "backend", "src/server.ts");
+    writeFileSync(
+      join(base, ".gsd", "PREFERENCES.md"),
+      `---\nversion: 1\nworkspace:\n  mode: parent\n  repositories:\n    frontend:\n      path: frontend\n    backend:\n      path: backend\n---\n`,
+      "utf-8",
+    );
+
+    // Same TTL window, no force: the changed workspace signature must miss the cache.
+    const refreshed = ensureCodebaseMapFresh(base, undefined, { ttlMs: 60_000 });
+    const written = readCodebaseMap(base)!;
+
+    assert.equal(refreshed.status, "updated");
+    assert.match(written, /## \[backend\]/);
+    assert.match(written, /`backend\/src\/server\.ts`/);
+  } finally {
+    cleanup(base);
+  }
+});

package/src/resources/extensions/gsd/tests/complete-milestone-excerpt.test.ts

@@ -12,7 +12,14 @@ import { tmpdir } from "node:os";
 
 import { buildSliceSummaryExcerpt, buildCompleteMilestonePrompt, buildValidateMilestonePrompt } from "../auto-prompts.ts";
 import { invalidateAllCaches } from "../cache.ts";
-import { closeDatabase, insertMilestone, openDatabase } from "../gsd-db.ts";
+import {
+  closeDatabase,
+  insertGateRow,
+  insertMilestone,
+  insertSlice,
+  openDatabase,
+  saveGateResult,
+} from "../gsd-db.ts";
 
 // ─── Fixture helpers ──────────────────────────────────────────────────────
 
@@ -366,6 +373,60 @@ test("validate-milestone prompt uses slice excerpts and on-demand paths instead
   );
 });
 
+test("validate-milestone prompt inlines persisted slice-level Q3/Q4 gate flags", async (t) => {
+  const base = createBase();
+  t.after(() => {
+    try { closeDatabase(); } catch { /* ignore */ }
+    cleanup(base);
+  });
+  invalidateAllCaches();
+
+  openDatabase(join(base, ".gsd", "gsd.db"));
+  insertMilestone({ id: "M001", title: "Test Milestone", status: "active" });
+  insertSlice({ id: "S01", milestoneId: "M001", title: "Risky Slice", status: "complete" });
+  insertGateRow({ milestoneId: "M001", sliceId: "S01", gateId: "Q3", scope: "slice" });
+  insertGateRow({ milestoneId: "M001", sliceId: "S01", gateId: "Q4", scope: "slice" });
+  insertGateRow({ milestoneId: "M001", sliceId: "S01", gateId: "Q8", scope: "slice" });
+  saveGateResult({
+    milestoneId: "M001",
+    sliceId: "S01",
+    gateId: "Q3",
+    verdict: "flag",
+    rationale: "New callback boundary.",
+    findings: "Re-check token exposure in the web callback.",
+  });
+  saveGateResult({
+    milestoneId: "M001",
+    sliceId: "S01",
+    gateId: "Q4",
+    verdict: "flag",
+    rationale: "Requirement touched but not re-tested.",
+    findings: "R012 must be re-tested; revisit decision D-3.",
+  });
+  saveGateResult({
+    milestoneId: "M001",
+    sliceId: "S01",
+    gateId: "Q8",
+    verdict: "flag",
+    rationale: "Operational readiness gap.",
+    findings: "Operational finding should not be milestone validation input.",
+  });
+  writeRoadmap(base, makeRoadmap());
+  writeSummary(base, "S01", makeFatSummary("S01"));
+
+  const prompt = await buildValidateMilestonePrompt("M001", "Test Milestone", base);
+
+  assert.match(prompt, /### Persisted Slice-Level Gate Flags \(from quality_gates\)/);
+  assert.match(prompt, /S01 \/ Q3 \(Threat Surface\) \/ flag/);
+  assert.match(prompt, /Re-check token exposure in the web callback\./);
+  assert.match(prompt, /S01 \/ Q4 \(Requirement Impact\) \/ flag/);
+  assert.match(prompt, /R012 must be re-tested; revisit decision D-3\./);
+  assert.ok(
+    !prompt.includes("Operational finding should not be milestone validation input."),
+    "validate-milestone should not inline unrelated Q8 gate findings",
+  );
+});
+
 test("validate-milestone prompt inlines planned verification classes as canonical rows", async (t) => {
   const base = createBase();
   t.after(() => {