fix: align feature marker seeding with GStack state

Wave-amended: seeding relocation re-applied to the composite action (v1.77 moved CI seeding out of the inline workflow steps the original commit edited); wiring tripwire re-pointed accordingly; stale marker comment updated

.github/actions/register-gstack-skills/action.yml

@@ -70,11 +70,9 @@ runs:
               "$HOME/.gstack/.telemetry-prompted" \
               "$HOME/.gstack/.proactive-prompted" \
               "$HOME/.gstack/.completeness-intro-seen" \
-              "$HOME/.gstack/.plan-tune-nudge-shown"
-        # These two resolve through the gstack root symlink into $REPO —
-        # untracked scratch in the CI checkout, exactly where the preamble looks.
-        touch "$SKILLS_DIR/gstack/.feature-prompted-continuous-checkpoint" \
-              "$SKILLS_DIR/gstack/.feature-prompted-model-overlay"
+              "$HOME/.gstack/.plan-tune-nudge-shown" \
+              "$HOME/.gstack/.feature-prompted-continuous-checkpoint" \
+              "$HOME/.gstack/.feature-prompted-model-overlay"
         echo "--- registry under $SKILLS_DIR ---"
         ls -la "$SKILLS_DIR/gstack"
         # ── Fail-fast verification ──────────────────────────────────────────

test/gstack-skill-start.test.ts

@@ -321,6 +321,7 @@ describe('gstack-skill-start behavior', () => {
       expect(checkpoint).toContain(
         `touch "${path.join(freshGh, '.feature-prompted-continuous-checkpoint')}"`,
       );
+      expect(checkpoint).not.toContain('GSTACK_INSTRUCTION_BEGIN: feature-overlay');
       expect(checkpoint).not.toContain(
         path.join(projectSkillRoot, '.feature-prompted-continuous-checkpoint'),
       );
@@ -334,7 +335,19 @@ describe('gstack-skill-start behavior', () => {
       expect(overlay).toContain(
         `touch "${path.join(freshGh, '.feature-prompted-model-overlay')}"`,
       );
+      expect(overlay).not.toContain('GSTACK_INSTRUCTION_BEGIN: feature-checkpoint');
       expect(overlay).not.toContain(path.join(projectSkillRoot, '.feature-prompted-model-overlay'));
+
+      fs.writeFileSync(path.join(freshGh, '.feature-prompted-model-overlay'), '');
+      const acknowledged = execFileSync(localStart, ['--skill', 'testskill'], {
+        encoding: 'utf-8',
+        cwd: projectRoot,
+        env,
+      });
+      expect(acknowledged).not.toContain('GSTACK_INSTRUCTION_BEGIN: feature-checkpoint');
+      expect(acknowledged).not.toContain('GSTACK_INSTRUCTION_BEGIN: feature-overlay');
+      expect(acknowledged).not.toContain('.feature-prompted-continuous-checkpoint');
+      expect(acknowledged).not.toContain('.feature-prompted-model-overlay');
     } finally {
       fs.rmSync(projectRoot, { recursive: true, force: true });
       fs.rmSync(freshGh, { recursive: true, force: true });

test/helpers/e2e-helpers.ts

@@ -324,7 +324,15 @@ if (evalsEnabled) {
   fs.mkdirSync(gstackDir, { recursive: true });
   // Marker list kept at parity with hermetic-env.ts's child-GSTACK_HOME seed
   // (the canonical set for the emission layer's gates).
-  for (const f of ['.activated', '.completeness-intro-seen', '.telemetry-prompted', '.proactive-prompted', '.first-loop-tip-shown']) {
+  for (const f of [
+    '.activated',
+    '.completeness-intro-seen',
+    '.telemetry-prompted',
+    '.proactive-prompted',
+    '.first-loop-tip-shown',
+    '.feature-prompted-continuous-checkpoint',
+    '.feature-prompted-model-overlay',
+  ]) {
     const p = path.join(gstackDir, f);
     if (!fs.existsSync(p)) fs.writeFileSync(p, '');
   }

test/helpers/hermetic-env.ts

@@ -217,7 +217,15 @@ export function getHermeticDirs(): HermeticDirs {
     // children — without these, the emission layer fires lake-intro/telemetry
     // prompts that burn turns and can stall PTY tests waiting on an answer.
     // Tests that exercise onboarding itself override GSTACK_HOME per-test.
-    for (const f of ['.activated', '.completeness-intro-seen', '.telemetry-prompted', '.proactive-prompted', '.first-loop-tip-shown']) {
+    for (const f of [
+      '.activated',
+      '.completeness-intro-seen',
+      '.telemetry-prompted',
+      '.proactive-prompted',
+      '.first-loop-tip-shown',
+      '.feature-prompted-continuous-checkpoint',
+      '.feature-prompted-model-overlay',
+    ]) {
       fs.writeFileSync(path.join(gstackHome, f), '');
     }
     // The privacy stop-gate is config-keyed, not marker-keyed: on machines

test/hermetic-wiring.test.ts

@@ -60,6 +60,34 @@ describe('hermetic wiring tripwire', () => {
     }
   });
 
+  test('feature prompt acknowledgements are seeded in GSTACK_HOME everywhere', () => {
+    const markers = [
+      '.feature-prompted-continuous-checkpoint',
+      '.feature-prompted-model-overlay',
+    ];
+    // CI seeding lives in the composite action (v1.77 moved it out of the
+    // inline workflow steps) — the workflows call the action, so one seeding
+    // site covers every lane.
+    const sources: Array<[string, number]> = [
+      ['test/helpers/hermetic-env.ts', 1],
+      ['test/helpers/e2e-helpers.ts', 1],
+      ['.github/actions/register-gstack-skills/action.yml', 1],
+    ];
+
+    for (const [rel, expectedCount] of sources) {
+      const src = read(rel);
+      for (const marker of markers) {
+        expect(src.split(marker).length - 1, `${rel}: ${marker}`).toBe(expectedCount);
+      }
+    }
+
+    for (const rel of ['.github/actions/register-gstack-skills/action.yml']) {
+      const src = read(rel);
+      expect(src).not.toContain('$SKILLS_DIR/gstack/.feature-prompted-');
+      for (const marker of markers) expect(src).toContain(`$HOME/.gstack/${marker}`);
+    }
+  });
+
   test('claude runners gate --strict-mcp-config on isHermeticEnabled()', () => {
     // Zero MCP servers for hermetic children; EVALS_HERMETIC=0 must restore
     // operator MCP along with the operator env (the flag may not be

test/setup-claude-skill-assets.test.ts

@@ -196,7 +196,7 @@ describe('two-class referenced-paths (ENG-OV7)', () => {
     const missing: string[] = [];
     for (const { fromSkill, skillName, rel } of collectRefs()) {
       if (skillName !== 'gstack') continue; // class 1
-      if (rel.startsWith('.')) continue; // runtime state markers (.feature-prompted-*, .git)
+      if (rel.startsWith('.')) continue; // runtime state (.git; feature markers now live in ~/.gstack — #2728)
       if (BUILT_ARTIFACT_ALLOWLIST.some((a) => rel === a || rel.startsWith(a))) continue;
       if (KNOWN_BROKEN_CLASS2[rel]) continue;
       if (!fs.existsSync(path.join(ROOT, rel))) {