Keep doctor repairs working on main-only repos and simplify managed ignores

bin/multiagent-safety.js

@@ -176,20 +176,8 @@ const GITIGNORE_MARKER_END = '# multiagent-safety:END';
 const MANAGED_GITIGNORE_PATHS = [
   '.omx/',
   '.omc/',
-  'scripts/agent-branch-start.sh',
-  'scripts/agent-branch-finish.sh',
-  'scripts/codex-agent.sh',
-  'scripts/review-bot-watch.sh',
-  'scripts/agent-worktree-prune.sh',
-  'scripts/agent-file-locks.py',
-  'scripts/guardex-env.sh',
-  'scripts/install-agent-git-hooks.sh',
-  'scripts/openspec/init-plan-workspace.sh',
-  'scripts/openspec/init-change-workspace.sh',
-  '.githooks/pre-commit',
-  '.githooks/pre-push',
-  '.githooks/post-merge',
-  '.githooks/post-checkout',
+  'scripts/*',
+  '.githooks',
   'oh-my-codex/',
   '.codex/skills/gitguardex/SKILL.md',
   '.codex/skills/guardex-merge-skills-to-dev/SKILL.md',
@@ -1592,7 +1580,7 @@ function finishDoctorSandboxBranch(blocked, metadata) {
 
   const finishResult = run(
     'bash',
-    [finishScript, '--branch', metadata.branch, '--via-pr', '--wait-for-merge'],
+    [finishScript, '--branch', metadata.branch, '--base', blocked.branch, '--via-pr', '--wait-for-merge'],
     { cwd: metadata.worktreePath, timeout: finishTimeoutMs },
   );
   if (isSpawnFailure(finishResult)) {

openspec/changes/agent-codex-ignore-scripts-star-and-githooks-2026-04-21-10-40/proposal.md

@@ -0,0 +1,21 @@
+## Why
+
+- The managed `.gitignore` block currently lists Guardex-owned `scripts/...` files and `.githooks/...` files one by one. That works, but it is noisy and drifts whenever new bootstrap files land under those directories.
+- Users expect `gx setup` / `gx doctor` to ignore the Guardex-managed script surface and the `.githooks` directory as a whole, not a hand-maintained list of individual files.
+- Users also expect `AGENTS.md` to come back when Guardex repairs a repo, especially on protected `main` where `gx doctor` has to repair through the sandbox flow.
+
+## What Changes
+
+- `bin/multiagent-safety.js`:
+  - Replace the per-file managed `.gitignore` entries for Guardex bootstrap scripts with a single `scripts/*` entry.
+  - Replace the per-file managed `.gitignore` entries for git hooks with a single `.githooks` entry.
+  - Keep protected-branch doctor auto-finish on the actual protected base branch instead of falling back to the default `dev` base.
+- `test/install.test.js`:
+  - Update setup assertions to require the wildcard-managed entries instead of the old per-file ignore lines.
+  - Extend protected-`main` and nested-repo doctor regressions so they prove `AGENTS.md` is restored and the wildcard `.gitignore` entries are repaired.
+
+## Impact
+
+- **New behavior**: `gx setup` / `gx doctor` write a smaller managed `.gitignore` block with `scripts/*` and `.githooks`.
+- **Repair proof**: the regression suite now pins `AGENTS.md` restoration for protected-`main` doctor flow and nested repo doctor flow, alongside the new wildcard ignore entries.
+- **Out of scope**: no package version change is needed here because `package.json` and `README.md` are already at `7.0.13`.

openspec/changes/agent-codex-ignore-scripts-star-and-githooks-2026-04-21-10-40/specs/ignore-scripts-star-and-githooks/spec.md

@@ -0,0 +1,36 @@
+## ADDED Requirements
+
+### Requirement: Managed `.gitignore` block ignores Guardex bootstrap directories with wildcard entries
+
+The marker-delimited `.gitignore` block written by `gx setup` and refreshed by `gx doctor` SHALL ignore the Guardex-managed bootstrap directories using stable directory-wide entries instead of enumerating individual files.
+
+#### Scenario: Fresh setup writes wildcard Guardex ignore entries
+- **GIVEN** a repo without an existing managed `.gitignore` block
+- **WHEN** the user runs `gx setup --target <repo>`
+- **THEN** the resulting managed block contains `scripts/*`
+- **AND** the resulting managed block contains `.githooks`
+
+#### Scenario: Repair refresh rewrites older per-file ignore entries
+- **GIVEN** a repo whose managed `.gitignore` block was written by an earlier Guardex version with per-file `scripts/...` and `.githooks/...` entries
+- **WHEN** the user runs `gx doctor --target <repo>` or `gx setup --target <repo>`
+- **THEN** the managed block is rewritten to contain `scripts/*` and `.githooks`
+- **AND** the managed block no longer depends on individual script or hook path entries for Guardex-managed files
+
+### Requirement: Doctor repairs restore `AGENTS.md` alongside wildcard ignore entries
+
+When `gx doctor` repairs Guardex drift, the repair flow SHALL restore `AGENTS.md` and the managed wildcard `.gitignore` entries together, including protected-branch sandbox repairs and nested-repo repairs.
+
+#### Scenario: Protected-main doctor restores AGENTS and wildcard ignore entries
+- **GIVEN** a protected-`main` repo where `AGENTS.md` has drifted away
+- **WHEN** the user runs `gx doctor --target <repo>`
+- **THEN** the repo regains `AGENTS.md`
+- **AND** its managed `.gitignore` block contains `scripts/*` and `.githooks`
+- **AND** the protected-branch finish flow keeps `main` as the base branch instead of falling back to `dev`
+
+#### Scenario: Recursive doctor restores nested repo AGENTS and wildcard ignore entries
+- **GIVEN** a parent repo with a nested standalone frontend repo on protected `main`
+- **AND** the nested repo is missing `AGENTS.md`
+- **AND** the nested repo's managed `.gitignore` block is missing `scripts/*` and `.githooks`
+- **WHEN** the user runs `gx doctor --target <parent-repo>`
+- **THEN** the nested repo regains `AGENTS.md`
+- **AND** the nested repo's managed `.gitignore` block contains `scripts/*` and `.githooks`

openspec/changes/agent-codex-ignore-scripts-star-and-githooks-2026-04-21-10-40/tasks.md

@@ -0,0 +1,22 @@
+## 1. Specification
+
+- [x] 1.1 Finalize proposal scope and acceptance criteria for `agent-codex-ignore-scripts-star-and-githooks-2026-04-21-10-40`.
+- [x] 1.2 Define normative requirements in `specs/ignore-scripts-star-and-githooks/spec.md`.
+
+## 2. Implementation
+
+- [x] 2.1 Replace per-file script entries in `MANAGED_GITIGNORE_PATHS` with `scripts/*`.
+- [x] 2.2 Replace per-file hook entries in `MANAGED_GITIGNORE_PATHS` with `.githooks`.
+- [x] 2.3 Keep doctor sandbox auto-finish on the current protected base branch so main-only repos do not fall back to `dev`.
+- [x] 2.4 Update setup and doctor regressions in `test/install.test.js` to pin the wildcard-managed entries and `AGENTS.md` restoration.
+- [x] 2.5 Confirm no version bump is needed because the repo is already on `7.0.13`.
+
+## 3. Verification
+
+- [x] 3.1 `node --check bin/multiagent-safety.js`
+- [x] 3.2 Focused `node --test` coverage for the affected setup/doctor cases.
+- [x] 3.3 `openspec validate agent-codex-ignore-scripts-star-and-githooks-2026-04-21-10-40 --type change --strict`
+
+## 4. Cleanup
+
+- [ ] 4.1 Finish the agent branch via PR merge + cleanup after verification.

test/install.test.js

@@ -407,15 +407,10 @@ test('setup provisions workflow files and repo config', () => {
 
   const gitignoreContent = fs.readFileSync(path.join(repoDir, '.gitignore'), 'utf8');
   assert.match(gitignoreContent, /# multiagent-safety:START/);
-  assert.match(gitignoreContent, /scripts\/agent-branch-start\.sh/);
-  assert.match(gitignoreContent, /scripts\/codex-agent\.sh/);
-  assert.match(gitignoreContent, /scripts\/review-bot-watch\.sh/);
-  assert.match(gitignoreContent, /scripts\/agent-file-locks\.py/);
-  assert.match(gitignoreContent, /scripts\/guardex-env\.sh/);
-  assert.match(gitignoreContent, /scripts\/openspec\/init-change-workspace\.sh/);
-  assert.match(gitignoreContent, /\.githooks\/pre-commit/);
-  assert.match(gitignoreContent, /\.githooks\/pre-push/);
-  assert.match(gitignoreContent, /\.githooks\/post-merge/);
+  assert.match(gitignoreContent, /^scripts\/\*$/m);
+  assert.match(gitignoreContent, /^\.githooks$/m);
+  assert.doesNotMatch(gitignoreContent, /^scripts\/agent-branch-start\.sh$/m);
+  assert.doesNotMatch(gitignoreContent, /^\.githooks\/pre-commit$/m);
   assert.match(gitignoreContent, /\.omx\//);
   assert.match(gitignoreContent, /\.omc\//);
   assert.match(gitignoreContent, /oh-my-codex\//);
@@ -1092,6 +1087,10 @@ exit 1
   assert.equal(result.status, 0, result.stderr || result.stdout);
   assert.match(result.stdout, /Auto-committed doctor repairs in sandbox branch/);
   assert.match(result.stdout, /Auto-finish flow completed for sandbox branch/);
+  assert.equal(fs.existsSync(path.join(repoDir, 'AGENTS.md')), true, 'protected main checkout should regain AGENTS.md');
+  const repairedRootGitignore = fs.readFileSync(path.join(repoDir, '.gitignore'), 'utf8');
+  assert.match(repairedRootGitignore, /^scripts\/\*$/m);
+  assert.match(repairedRootGitignore, /^\.githooks$/m);
 
   const createdBranch = extractCreatedBranch(result.stdout);
   result = runCmd('git', ['show-ref', '--verify', '--quiet', `refs/heads/${createdBranch}`], repoDir);
@@ -2360,6 +2359,8 @@ test('setup appends managed gitignore block without clobbering existing entries'
   const first = fs.readFileSync(path.join(repoDir, '.gitignore'), 'utf8');
   assert.match(first, /node_modules\//);
   assert.match(first, /# multiagent-safety:START/);
+  assert.match(first, /^scripts\/\*$/m);
+  assert.match(first, /^\.githooks$/m);
   assert.match(first, /# multiagent-safety:END/);
 
   result = runNode(['setup', '--target', repoDir, '--no-global-install'], repoDir);
@@ -3913,19 +3914,31 @@ test('doctor repairs setup drift and confirms repo is safe', () => {
 test('doctor recurses into nested frontend repos and repairs protected-main drift', () => {
   const repoDir = initRepo();
   const frontendDir = path.join(repoDir, 'frontend');
+  const frontendGitignorePath = path.join(frontendDir, '.gitignore');
   fs.mkdirSync(frontendDir, { recursive: true });
 
   let result = runCmd('git', ['init', '-b', 'main'], frontendDir);
   assert.equal(result.status, 0, result.stderr || result.stdout);
+  fs.writeFileSync(path.join(frontendDir, 'package.json'), '{}\n', 'utf8');
   seedCommit(frontendDir);
 
   result = runNode(['setup', '--target', repoDir, '--no-global-install'], repoDir);
   assert.equal(result.status, 0, result.stderr || result.stdout);
   assert.equal(fs.existsSync(path.join(frontendDir, 'AGENTS.md')), true, 'nested frontend should be bootstrapped by setup');
+  const initialFrontendGitignore = fs.readFileSync(frontendGitignorePath, 'utf8');
+  assert.match(initialFrontendGitignore, /^scripts\/\*$/m);
+  assert.match(initialFrontendGitignore, /^\.githooks$/m);
 
   fs.rmSync(path.join(frontendDir, 'AGENTS.md'));
   fs.rmSync(path.join(frontendDir, 'scripts', 'agent-branch-start.sh'));
   fs.rmSync(path.join(frontendDir, '.githooks', 'pre-commit'));
+  fs.writeFileSync(
+    frontendGitignorePath,
+    initialFrontendGitignore
+      .replace(/^scripts\/\*\n/m, '')
+      .replace(/^\.githooks\n/m, ''),
+    'utf8',
+  );
   fs.writeFileSync(path.join(frontendDir, '.omx', 'state', 'agent-file-locks.json'), '{broken json', 'utf8');
 
   result = runNode(['doctor', '--target', repoDir], repoDir);
@@ -3940,6 +3953,9 @@ test('doctor recurses into nested frontend repos and repairs protected-main drif
     true,
     'nested frontend sandbox starter should be restored',
   );
+  const repairedFrontendGitignore = fs.readFileSync(frontendGitignorePath, 'utf8');
+  assert.match(repairedFrontendGitignore, /^scripts\/\*$/m);
+  assert.match(repairedFrontendGitignore, /^\.githooks$/m);
   const repairedFrontendHook = fs.readFileSync(path.join(frontendDir, '.githooks', 'pre-commit'), 'utf8');
   assert.match(repairedFrontendHook, /AGENTS\.md\|\.gitignore/);