diff --git a/bin/gstack-skill-start b/bin/gstack-skill-start
index d63c47de3..3da95c78a 100755
--- a/bin/gstack-skill-start
+++ b/bin/gstack-skill-start
@@ -362,14 +362,16 @@ if [ -n "$_UPD" ]; then
 The update-check output above applies. If it shows \`UPGRADE_AVAILABLE <old> <new>\`: read \`$_ROOT_DIR/gstack-upgrade/SKILL.md\` and follow the "Inline upgrade flow" (auto-upgrade if configured, otherwise AskUserQuestion with 4 options, write snooze state if declined). If it shows \`JUST_UPGRADED <from> <to>\`: print "Running gstack v{to} (just updated!)". If \`SPAWNED_SESSION\` is true, skip feature discovery. After upgrade prompts, continue the workflow.
 EOI
 fi
-# Feature discovery (one prompt per session, marker-gated).
-if [ ! -f "$_ROOT_DIR/.feature-prompted-continuous-checkpoint" ]; then
+# Feature discovery (one prompt per session, marker-gated). These are
+# machine-local UX acknowledgements, so keep them in GSTACK_HOME rather than
+# beside an install path that may resolve through a project-local symlink.
+if [ ! -f "$_GH/.feature-prompted-continuous-checkpoint" ]; then
   _emit_block feature-checkpoint <<EOI
-Feature discovery: AskUserQuestion for Continuous checkpoint auto-commits. If accepted, run \`$_BIN/gstack-config set checkpoint_mode continuous\`. Always run: \`touch "$_ROOT_DIR/.feature-prompted-continuous-checkpoint"\`.
+Feature discovery: AskUserQuestion for Continuous checkpoint auto-commits. If accepted, run \`$_BIN/gstack-config set checkpoint_mode continuous\`. Always run: \`touch "$_GH/.feature-prompted-continuous-checkpoint"\`.
 EOI
-elif [ ! -f "$_ROOT_DIR/.feature-prompted-model-overlay" ]; then
+elif [ ! -f "$_GH/.feature-prompted-model-overlay" ]; then
   _emit_block feature-overlay <<EOI
-Feature discovery: inform "Model overlays are active. MODEL_OVERLAY shows the patch." Always run: \`touch "$_ROOT_DIR/.feature-prompted-model-overlay"\`.
+Feature discovery: inform "Model overlays are active. MODEL_OVERLAY shows the patch." Always run: \`touch "$_GH/.feature-prompted-model-overlay"\`.
 EOI
 fi
 
diff --git a/test/gstack-skill-start.test.ts b/test/gstack-skill-start.test.ts
index fcc069d64..46acf6792 100644
--- a/test/gstack-skill-start.test.ts
+++ b/test/gstack-skill-start.test.ts
@@ -302,6 +302,45 @@ describe('gstack-skill-start behavior', () => {
     }
   });
 
+  test('feature acknowledgement markers stay in GSTACK_HOME through a project-local bin symlink', () => {
+    const projectRoot = fs.mkdtempSync(path.join(os.tmpdir(), 'gstack-ss-project-'));
+    const projectSkillRoot = path.join(projectRoot, '.agents', 'skills', 'gstack');
+    const freshGh = fs.mkdtempSync(path.join(os.tmpdir(), 'gstack-ss-feature-state-'));
+    fs.mkdirSync(projectSkillRoot, { recursive: true });
+    fs.symlinkSync(path.join(ROOT, 'bin'), path.join(projectSkillRoot, 'bin'), 'dir');
+    fs.writeFileSync(path.join(freshGh, 'config.yaml'), 'update_check: false\n');
+
+    const localStart = path.join(projectSkillRoot, 'bin', 'gstack-skill-start');
+    const env = { PATH: process.env.PATH!, HOME: tmpHome, GSTACK_HOME: freshGh };
+    try {
+      const checkpoint = execFileSync(localStart, ['--skill', 'testskill'], {
+        encoding: 'utf-8',
+        cwd: projectRoot,
+        env,
+      });
+      expect(checkpoint).toContain(
+        `touch "${path.join(freshGh, '.feature-prompted-continuous-checkpoint')}"`,
+      );
+      expect(checkpoint).not.toContain(
+        path.join(projectSkillRoot, '.feature-prompted-continuous-checkpoint'),
+      );
+
+      fs.writeFileSync(path.join(freshGh, '.feature-prompted-continuous-checkpoint'), '');
+      const overlay = execFileSync(localStart, ['--skill', 'testskill'], {
+        encoding: 'utf-8',
+        cwd: projectRoot,
+        env,
+      });
+      expect(overlay).toContain(
+        `touch "${path.join(freshGh, '.feature-prompted-model-overlay')}"`,
+      );
+      expect(overlay).not.toContain(path.join(projectSkillRoot, '.feature-prompted-model-overlay'));
+    } finally {
+      fs.rmSync(projectRoot, { recursive: true, force: true });
+      fs.rmSync(freshGh, { recursive: true, force: true });
+    }
+  });
+
   test('MODEL_OVERLAY echoes the --model argument', () => {
     const out = runStart(['--model', 'opus']);
     expect(out).toMatch(/^MODEL_OVERLAY: opus$/m);