diff --git a/bin/gstack-team-init b/bin/gstack-team-init
index a416d40fa..bf5a07428 100755
--- a/bin/gstack-team-init
+++ b/bin/gstack-team-init
@@ -220,6 +220,9 @@ HOOK_EOF
     # registered successfully. Other project hooks are left untouched.
     if [ -e "$HOOKS_DIR/check-gstack.sh" ] || [ -L "$HOOKS_DIR/check-gstack.sh" ]; then
       rm "$HOOKS_DIR/check-gstack.sh"
+      if (cd "$REPO_ROOT" && git ls-files --error-unmatch -- .claude/hooks/check-gstack.sh >/dev/null 2>&1); then
+        GENERATED+=(".claude/hooks/check-gstack.sh")
+      fi
       echo "  - .claude/hooks/check-gstack.sh — removed legacy enforcement hook"
     fi
   else
diff --git a/implementation-notes.html b/implementation-notes.html
index d4e2fad0f..c740af189 100644
--- a/implementation-notes.html
+++ b/implementation-notes.html
@@ -18,7 +18,7 @@
       <li>The generated hook resolves the user home in <code>HOME</code>, <code>USERPROFILE</code>, then <code>os.homedir()</code> order so POSIX, Git Bash, PowerShell, and cmd runners use the expected global install root.</li>
       <li>The hook contract follows <code>docs/spikes/claude-code-hook-mutation.md</code>: pass-through writes <code>{}</code>; denial writes a <code>hookSpecificOutput</code> object for <code>PreToolUse</code> with <code>permissionDecision: "deny"</code>.</li>
       <li>Missing or unreadable gstack is an intentional denial with exit code zero. Install instructions are present in stderr and <code>permissionDecisionReason</code>, so the runner does not report a hook execution error.</li>
-      <li>Rerunning required mode replaces a matching legacy <code>check-gstack.sh</code> registration, removes duplicate matching registrations, and deletes the obsolete Bash hook only after the CommonJS hook is generated and registered successfully. Unrelated project hooks remain unchanged.</li>
+      <li>Rerunning required mode replaces a matching legacy <code>check-gstack.sh</code> registration, removes duplicate matching registrations, and deletes the obsolete Bash hook only after the CommonJS hook is generated and registered successfully. If Git tracks the deleted hook, the printed <code>git add</code> command includes its path so the suggested migration commit stages the deletion; untracked removed hooks are omitted because they have no index change. Unrelated project hooks remain unchanged.</li>
     </ul>
 
     <h2>Deviations</h2>
diff --git a/test/team-mode.test.ts b/test/team-mode.test.ts
index b555f471c..17c815160 100644
--- a/test/team-mode.test.ts
+++ b/test/team-mode.test.ts
@@ -302,7 +302,7 @@ describe('gstack-team-init', () => {
   });
 
   test('required: creates enforcement hook', () => {
-    run(`${TEAM_INIT} required`, { cwd: tmpDir });
+    const result = run(`${TEAM_INIT} required`, { cwd: tmpDir });
     const hookPath = path.join(tmpDir, '.claude', 'hooks', 'check-gstack.cjs');
     expect(fs.existsSync(hookPath)).toBe(true);
     expect(
@@ -319,6 +319,7 @@ describe('gstack-team-init', () => {
     expect(hook).toContain("permissionDecision: 'deny'");
     expect(hook).toContain('BLOCKED: gstack is not installed');
     expect(hook).not.toContain('#!/bin/bash');
+    expect(result.stdout).not.toMatch(/git add .*check-gstack\.sh/);
   });
 
   test('required: registers one shell-neutral project hook', () => {
@@ -534,22 +535,45 @@ describe('gstack-team-init', () => {
     execSync('git add .claude', { cwd: tmpDir });
     execSync('git commit -m "add legacy hook"', { cwd: tmpDir });
 
-    run(`${TEAM_INIT} required`, { cwd: tmpDir });
+    const migration = run(`${TEAM_INIT} required`, { cwd: tmpDir });
     expect(fs.existsSync(legacyHook)).toBe(false);
     expect(fs.readFileSync(unrelatedHook, 'utf-8')).toBe(unrelatedHookContents);
+    const suggestedGitAdd = migration.stdout
+      .split('\n')
+      .find(line => line.startsWith('  git add '))
+      ?.trim();
+    if (!suggestedGitAdd) {
+      throw new Error('gstack-team-init did not print a git add command');
+    }
+    expect(suggestedGitAdd.split(/\s+/)).toContain(
+      '.claude/hooks/check-gstack.sh',
+    );
+    execSync(suggestedGitAdd, { cwd: tmpDir });
+    execSync('git commit -m "migrate required hook"', { cwd: tmpDir });
+    expect(
+      execSync('git status --short', { cwd: tmpDir, encoding: 'utf-8' }),
+    ).toBe('');
 
-    run(`${TEAM_INIT} required`, { cwd: tmpDir });
+    const rerun = run(`${TEAM_INIT} required`, { cwd: tmpDir });
     const settings = JSON.parse(
       fs.readFileSync(path.join(tmpDir, '.claude', 'settings.json'), 'utf-8'),
     );
     expect(fs.existsSync(legacyHook)).toBe(false);
     expect(fs.readFileSync(unrelatedHook, 'utf-8')).toBe(unrelatedHookContents);
+    const rerunGitAdd = rerun.stdout
+      .split('\n')
+      .find(line => line.startsWith('  git add '))
+      ?.trim();
+    if (!rerunGitAdd) {
+      throw new Error('gstack-team-init rerun did not print a git add command');
+    }
+    expect(rerunGitAdd.split(/\s+/)).not.toContain(
+      '.claude/hooks/check-gstack.sh',
+    );
+    execSync(rerunGitAdd, { cwd: tmpDir });
     expect(
-      execSync('git status --short -- .claude/hooks/check-gstack.sh', {
-        cwd: tmpDir,
-        encoding: 'utf-8',
-      }),
-    ).toBe(' D .claude/hooks/check-gstack.sh\n');
+      execSync('git status --short', { cwd: tmpDir, encoding: 'utf-8' }),
+    ).toBe('');
     expect(settings.hooks.PreToolUse).toHaveLength(1);
     expect(settings.hooks.PreToolUse[0].hooks).toHaveLength(1);
     expect(settings.hooks.PreToolUse[0].hooks[0].command).toContain(