fix(hooks): trust Codex hooks and share project hooks across worktrees

docs/designs/data-directory-layout.md

@@ -495,7 +495,14 @@ every checkout, so that is where they live now:
 ├── learnings-wt/                              getWorktreeDir → <dataHome>/<dirname>
 ├── reports-wt/                                (the side-branch locks sit beside them)
 ├── pending-learnings/                         pendingLearningsDir → <dataHome>/pending-learnings
+├── managed-main-checkout-hooks.json           team hooks teamai wrote ungated into the main checkout's Claude Code / Codex
+│                                              settings, shared by every checkout (#955; the built-in hooks stay in HOME)
+│                                              project toolPaths choose the files; Claude uses settings.local.json beside its settings file
+│                                              Codex records event, matcher-group position and complete rendered entry; unique definitions recover moved entries
+│                                              legacy ownership matches event/matcher/command uniquely, ignoring unrecorded timeout/context options
+│                                              pre-#370 Codex ownership is imported from <main>/.teamai/managed-hooks.json before reconcile/removal
 └── workspaces/<managedMcpWorkspaceId(root)>/
+    ├── managed-main-checkout-hooks.json       bare repositories only: this workspace owns its Claude / Codex team-hook files and trust target
     ├── managed-mcp.json                       managedMcpManifestPath, one per checkout; Copilot placement is true for bare, false for keyed, absent when unproven
     ├── managed-mcp-files.json                 resolvedMcpFilesPath: project MCP configs teamai may have written a resolved ${VAR} to, and whether
     │                                          the paths earlier teamai.yaml revisions mapped were read; one of those git tracks is marked tracked (#882);

skill-data/core/references/troubleshooting.md

@@ -28,8 +28,14 @@ This is the #1 onboarding issue. In order:
    ```bash
    teamai hooks inject
    ```
-4. **Wrong scope?** Project-scope hooks are written to your HOME tool settings
-   (e.g. `~/.claude/settings.json`), not the project folder — that is intentional.
+4. **Wrong scope?** Project-scope built-in hooks are written to your HOME tool
+   settings (e.g. `~/.claude/settings.json`), not the project folder; the team's own
+   hooks for Claude Code and Codex go to the main checkout
+   (`.claude/settings.local.json`, `.codex/hooks.json`). That is intentional.
+   Removal also checks existing Claude/Codex main-checkout hook files when the
+   HOME tool root is missing or relocated.
+   In project scope, `teamai hooks remove` preserves other projects' gated team
+   hooks in HOME, while removing the shared built-in hooks.
    If you initialized project scope but expected machine-wide resources, re-run
    with `--scope user`.
 5. **Tool has no hook surface** (e.g. Gemini CLI, JoyCode): there is no auto-sync;
@@ -142,7 +148,7 @@ broken machine):
 | Tool                  | Hooks status              | Why                                                                 |
 |-----------------------|---------------------------|---------------------------------------------------------------------|
 | Claude Code (`claude`)| Installed                 | Fully supported — this is the main, working path                    |
-| Codex                 | Written but **trust-gated** or skipped | Codex gates non-managed hooks behind an explicit trust step; `teamai doctor` prints a reminder to trust them |
+| Codex                 | Installed and trusted     | Codex runs only trusted hooks; teamai trusts the ones it writes through `codex app-server`, and `teamai doctor` names any Codex will not run |
 | Cursor                | Installed                 | Also runs `~/.claude/settings.json`. That copy exits only when `~/.cursor/hooks.json` or the project `.cursor/hooks.json` contains `--tool cursor` |
 | Copilot CLI           | Installed in self mode    | Also runs a trusted project's `.claude/settings.json`. That copy exits only when `.github/hooks/teamai.json` contains `--tool copilot`. `COPILOT_CLI` alone does not skip |
 | CodeBuddy / WorkBuddy | Installed                 | Claude-format hooks in their own `settings.json`                    |
@@ -161,11 +167,23 @@ step — do not assume auto-sync just works.
 
 ### Codex
 
-Codex gates non-managed hooks behind an explicit **trust** step. `teamai init` /
-`teamai hooks inject` may write the hooks, but Codex won't run them until the user
-trusts them (`teamai doctor` prints a reminder when it detects this). Guide the
-user to trust the teamai hooks in Codex, then reopen a session. Until then, run
-`teamai pull` manually.
+Codex runs a non-managed hook only once it is **trusted**. `teamai init`, `pull`
+and `teamai hooks inject` trust the hooks they write (and, in a project, the main
+checkout, or the current worktree for a bare repository) through `codex app-server`.
+Trust written by a session-start pull applies from the next Codex session. `teamai doctor` names any teamai hook Codex will not
+run. Then: run `teamai pull`; if `codex` is not on PATH or `codexTrustEnabled: false`
+is set in `config.yaml`, guide the user to trust the teamai hooks in Codex `/hooks`,
+then reopen a session. A new linked worktree gets the team hooks from its second
+Codex session (the first creates its `.codex/`). Member hooks with the same command
+are preserved and remain untouched by automatic trust. Codex ownership uses the
+recorded event, position and complete entry. A moved entry is recovered only by a
+unique full-definition match. Legacy records recover only a unique event, matcher
+and command match; `timeout` and `additionalContextLimit` were not recorded.
+Pre-#370 project Codex ownership is imported from the main checkout's
+`.teamai/managed-hooks.json` before reconciliation or direct removal.
+Unrecorded or ambiguous legacy team-hook copies are preserved. Project hook paths follow `toolPaths`;
+Claude uses `settings.local.json` beside its configured settings file. A custom
+Codex path that Codex does not load is reported as `not loaded` by doctor.
 
 ### Cursor
 

skill-data/setup/SKILL.md

@@ -46,8 +46,9 @@ and create-repo URLs, and the per-provider caveats, and points at
    install. Let `teamai init` set up every AI tool already installed (omitting
    `--agent` gives an interactive picker; select all detected tools). **After init,
    report which agents were set up** — in the user's language, which tools now
-   auto-start TeamAI, and which detected tools were skipped and why (e.g. Codex
-   trust-gate, CodeBuddy design). Verify the real per-tool result with
+   auto-start TeamAI, which detected tools were skipped and why (e.g. CodeBuddy
+   design), and any installed hooks that still need trust (e.g. Codex with
+   automatic trust disabled or unavailable). Verify the real per-tool result with
    `teamai doctor` and `teamai hooks list`.
 3. **After init, resources appear on the NEXT session.** `teamai init` injects a
    session-start hook that auto-runs `teamai pull`. Empty skills/rules directories

skill-data/setup/references/setup-admin.md

@@ -213,8 +213,9 @@ login` run in an interactive shell (see Step 3).
 Claude Code"). Omitting `--agent` gives an interactive picker — select **every AI
 tool already installed** on the machine. Then **report back which agents were set
 up**, in the user's language: name the tools that will now auto-start TeamAI, and
-any detected tool that was skipped and why (e.g. Codex trust-gate,
-CodeBuddy/WorkBuddy by design — see the troubleshooting reference, `"$(teamai skill path core)/references/troubleshooting.md"`).
+any detected tool that was skipped and why (e.g. CodeBuddy/WorkBuddy by design),
+and any installed hooks that still need trust (e.g. Codex with automatic trust
+disabled or unavailable). See the troubleshooting reference, `"$(teamai skill path core)/references/troubleshooting.md"`.
 
 ## Step 6 — Verify with doctor
 

src/__tests__/anchors.test.ts

@@ -201,6 +201,7 @@ describe('defaultProjectSlug (#809)', () => {
       const checkout = path.join(base, 'bare-layout', wt);
       git(bare, 'worktree', 'add', '-q', checkout);
       expect((await resolveAnchors(checkout))?.projectAnchor).toBe(bare);
+      expect((await resolveAnchors(checkout))?.projectAnchorIsBare).toBe(true);
       expect(await defaultProjectSlug(checkout)).toBe('bare-layout');
     }
     const sub = path.join(base, 'bare-layout', 'main', 'pkg');

src/__tests__/bootstrap-self.test.ts

@@ -1,8 +1,18 @@
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
 import fs from 'node:fs';
 import path from 'node:path';
 import os from 'node:os';
 import YAML from 'yaml';
+vi.mock('../providers/index.js', async (importOriginal) => ({
+  ...await importOriginal<typeof import('../providers/index.js')>(),
+  getProvider: vi.fn(() => ({
+    isAuthenticated: () => true,
+    authenticate: async () => 'tester',
+    parseRepoInput: (remote: string) => ({ httpsUrl: remote }),
+  })),
+}));
+
+import { installFakeCodex, readFakeCodexState } from './helpers/fake-codex.js';
 import { bootstrapSelfRepo } from '../bootstrap.js';
 import { detectProjectConfig } from '../config.js';
 
@@ -13,6 +23,7 @@ beforeEach(() => {
 });
 
 afterEach(() => {
+  vi.unstubAllEnvs();
   fs.rmSync(tmpDir, { recursive: true, force: true });
 });
 
@@ -33,6 +44,32 @@ describe('bootstrapSelfRepo', () => {
     expect(result).toBe('skip');
   });
 
+  it('trusts self project hooks during a silent bootstrap', async () => {
+    tmpDir = fs.realpathSync.native(tmpDir);
+    const home = path.join(tmpDir, 'home');
+    const project = path.join(tmpDir, 'project');
+    const teamaiDir = path.join(project, '.teamai');
+    const codexHome = path.join(home, '.codex');
+    fs.mkdirSync(teamaiDir, { recursive: true });
+    fs.mkdirSync(codexHome, { recursive: true });
+    const fakeBin = installFakeCodex();
+    vi.stubEnv('HOME', home);
+    vi.stubEnv('PATH', `${fakeBin}${path.delimiter}${process.env.PATH ?? ''}`);
+    fs.writeFileSync(path.join(teamaiDir, 'teamai.yaml'), YAML.stringify({
+      team: 'test', mode: 'self', repo: 'https://github.com/acme/app.git', provider: 'github',
+      toolPaths: { codex: { skills: '.codex/skills', settings: '.codex/hooks.json' } },
+    }));
+    try {
+      expect(await bootstrapSelfRepo(project, { silent: true })).toBe('bootstrapped');
+      const state = readFakeCodexState(codexHome);
+      expect(state.projects[project]).toEqual({ trust_level: 'trusted' });
+      expect(Object.keys(state.hooksState).length).toBeGreaterThan(0);
+      expect(Object.keys(state.hooksState).every((key) => key.startsWith(path.join(project, '.codex', 'hooks.json')))).toBe(true);
+    } finally {
+      fs.rmSync(fakeBin, { recursive: true, force: true });
+    }
+  });
+
   it("returns 'already' when a local config.yaml is already present", async () => {
     const teamaiDir = path.join(tmpDir, '.teamai');
     fs.mkdirSync(teamaiDir, { recursive: true });