fix(#3964): route init's waiting-signal, codebase, and skill-manifest paths through the project-aware resolver (#3971)

* test(#3964): waiting_signal, codebase_dir, and skill-manifest must be project-scoped

* fix(#3964): route waiting_signal, codebase_dir, and skill-manifest through the project-aware resolver

* chore(#3964): changeset fragment (pr number backfilled after PR creation)

* chore(#3964): backfill changeset PR number (3971)

* test(#3964): assert on the POSIX-normalized codebase_dir across platforms

---------

Co-authored-by: sim <sim@local>

src/artifacts.cts

@@ -28,6 +28,7 @@ export const CANONICAL_EXACT: ReadonlySet<string> = new Set([
   'STATE-ARCHIVE.md', // state.cts's cmdStatePrune writes this at the .planning/ root
   'milestone.lock', // #3311: milestone (phase + session) claim (src/milestone-lock.cts); persistent, unlike the transient STATE.md.lock/WAITING.json
   'state.json', // #3227: machine-readable state contract published at step boundaries (src/state-contract.cts)
+  'skill-manifest.json', // init.cts routeSkillManifest --write (project-scoped planning root, #3964)
 ]);
 
 // Pattern-match canonical file names (regex tests on the basename)

src/init.cts

@@ -2308,7 +2308,12 @@ function cmdInitMilestoneOp(cwd: string, raw: boolean): void {
 function cmdInitMapCodebase(cwd: string, raw: boolean): void {
   const config = loadConfig(cwd);
 
-  const codebaseDir = path.join(planningRoot(cwd), 'codebase');
+  // #3964: scoped like the payload's own codebase_dir/codebase_dir_exists
+  // below (and verify.cts's codebase drift check) — has_maps/existing_maps
+  // reading the flat root made the same payload claim a scoped codebase dir
+  // exists while reporting zero maps, so map-codebase's Refresh/Skip gate
+  // always forced a re-map under GSD_PROJECT.
+  const codebaseDir = path.join(planningDir(cwd), 'codebase');
   let existingMaps: string[] = [];
   try {
     existingMaps = fs.readdirSync(codebaseDir).filter((f) => f.endsWith('.md'));
@@ -2328,13 +2333,16 @@ function cmdInitMapCodebase(cwd: string, raw: boolean): void {
     timestamp: realClock.nowIso(),
 
     // #2376: absolute — see comment on phase_dir in cmdInitExecutePhase.
-    codebase_dir: toPosixPath(path.join(planningRoot(cwd), 'codebase')),
+    // #3964: scoped like verify.cts's codebase drift check (planningDir, not
+    // the flat planningRoot) so the two surfaces cannot disagree under
+    // GSD_PROJECT.
+    codebase_dir: toPosixPath(path.join(planningDir(cwd), 'codebase')),
 
     existing_maps: existingMaps,
     has_maps: existingMaps.length > 0,
 
     planning_exists: pathExistsInternal(cwd, '.planning'),
-    codebase_dir_exists: pathExistsInternal(cwd, '.planning/codebase'),
+    codebase_dir_exists: pathExistsInternal(cwd, toPosixPath(path.relative(cwd, path.join(planningDir(cwd), 'codebase')))),
   };
 
   output(withProjectRoot(cwd, result), raw);
@@ -2584,7 +2592,13 @@ function cmdInitManager(cwd: string, raw: boolean): void {
 
   let waitingSignal: unknown = null;
   try {
-    const waitingPath = path.join(cwd, '.planning', 'WAITING.json');
+    // #3964: mirror cmdSignalWaiting's write locations exactly — `.gsd/`
+    // first when it exists, else the project-aware planning dir — so the
+    // signal is read from the project (and location) it is written to.
+    const gsdWaiting = path.join(cwd, '.gsd', 'WAITING.json');
+    const waitingPath = fs.existsSync(path.join(cwd, '.gsd'))
+      ? gsdWaiting
+      : path.join(planningDir(cwd), 'WAITING.json');
     const waitingRaw = platformReadSync(waitingPath);
     if (waitingRaw !== null) {
       waitingSignal = JSON.parse(waitingRaw);
@@ -4001,7 +4015,9 @@ function cmdSkillManifest(cwd: string, args: string[], raw: boolean): void {
   const manifest = buildSkillManifest(cwd, skillsDir);
 
   if (args.includes('--write')) {
-    const planDir = path.join(cwd, '.planning');
+    // #3964: write beside the project's own artifacts (planningDir is
+    // project- and workstream-aware), not the flat root.
+    const planDir = planningDir(cwd);
     if (fs.existsSync(planDir)) {
       const manifestPath = path.join(planDir, 'skill-manifest.json');
       platformWriteSync(manifestPath, JSON.stringify(manifest, null, 2));

src/onboard-projection.cts

@@ -200,7 +200,11 @@ function listPlanningDocCandidates(cwd: string): string[] {
 }
 
 function listCodebaseMapFiles(cwd: string): string[] {
-  const codebaseDir = path.join(planningRoot(cwd), 'codebase');
+  // #3964: project-scoped, agreeing with init's map-codebase surface and
+  // verify.cts's codebase drift check — a flat-root read made
+  // has_codebase_map/needs_codebase_map answer for the wrong project under
+  // GSD_PROJECT.
+  const codebaseDir = path.join(planningDir(cwd), 'codebase');
   if (!fs.existsSync(codebaseDir)) return [];
   return REQUIRED_CODEBASE_MAP_FILES.filter((file) =>
     fs.existsSync(path.join(codebaseDir, file)),