Keep the setup alias task log truthful before finish

README.md

@@ -279,6 +279,8 @@ Setup auto-installs into every nested git repo (e.g. `apps/*/.git`). Submodules
 ```sh
 gx setup --target /mainfolder
 gx setup --target /mainfolder --no-recursive
+gx setup --target /mainfolder --current
+gx doctor --target /mainfolder --current
 ```
 
 ### Fresh repos + Docker Compose

openspec/changes/agent-codex-setup-current-single-repo-alias-2026-04-22-13-48/proposal.md

@@ -0,0 +1,18 @@
+## Why
+
+- `gx setup` recurses into nested repos by default, so operators need a short explicit way to keep a bootstrap or repair run scoped to just the target repo.
+- `--no-recursive` already provides that behavior, but users naturally reach for `--current` after learning `gx doctor --current`.
+- The current mismatch makes `setup` and `doctor` feel inconsistent even though they share the same repo-traversal model.
+
+## What Changes
+
+- Accept `--current` as a top-level-only alias for repo traversal in `gx setup`.
+- Keep `gx doctor --current` working through the same shared traversal parser instead of a command-local special case.
+- Update setup-facing operator copy to mention `--current` alongside `--no-recursive`.
+- Add a regression proving nested repos under the target path stay untouched when `gx setup --current` is used.
+
+## Impact
+
+- Affected surface: `src/cli/main.js`, `src/context.js`, `test/setup.test.js`, `README.md`.
+- Expected outcome: `gx setup --current` and `gx doctor --current` both scope work to the target repo only.
+- Risk: low, because the alias reuses the existing non-recursive traversal path.

openspec/changes/agent-codex-setup-current-single-repo-alias-2026-04-22-13-48/specs/nested-repo-setup/spec.md

@@ -0,0 +1,10 @@
+## ADDED Requirements
+
+### Requirement: setup current alias limits bootstrap to the target repo
+The system SHALL support `gx setup --current` as an alias for the existing top-level-only traversal path.
+
+#### Scenario: current alias skips nested repo installs
+- **GIVEN** a parent repo contains a nested standalone git repo
+- **WHEN** `gx setup --target <parent-repo> --current` runs
+- **THEN** the setup flow SHALL install or repair only `<parent-repo>`
+- **AND** the nested repo SHALL not be traversed or modified during that run.

openspec/changes/agent-codex-setup-current-single-repo-alias-2026-04-22-13-48/tasks.md

@@ -0,0 +1,34 @@
+## Definition of Done
+
+This change is complete only when **all** of the following are true:
+
+- Every checkbox below is checked.
+- The agent branch reaches `MERGED` state on `origin` and the PR URL + state are recorded in the completion handoff.
+- If any step blocks, add a `BLOCKED:` line under section 4 and stop.
+
+Handoff: change=`agent-codex-setup-current-single-repo-alias-2026-04-22-13-48`; branch=`agent/codex/setup-current-single-repo-alias-2026-04-22-13-48`; scope=`OpenSpec change docs, setup traversal parsing, setup regression coverage, operator-facing setup copy`; action=`accept --current as the top-repo-only setup alias and keep traversal messaging aligned with doctor`.
+
+## 1. Specification
+
+- [x] 1.1 Capture the `gx setup --current` alias scope and acceptance criteria.
+- [x] 1.2 Add normative OpenSpec coverage for the setup single-repo alias behavior.
+
+## 2. Implementation
+
+- [x] 2.1 Accept `--current` as a setup alias for the existing top-level-only traversal path.
+- [x] 2.2 Update setup-facing help/output/docs to advertise `--current`.
+- [x] 2.3 Add a regression proving nested repos under the target path stay untouched.
+
+## 3. Verification
+
+- [x] 3.1 Run `node --check bin/multiagent-safety.js`. Result: passed.
+- [x] 3.2 Run `node --test test/setup.test.js`. Result: passed (`42/42` tests, including `setup --current limits install to the top-level repo`).
+- [x] 3.3 Run `openspec validate agent-codex-setup-current-single-repo-alias-2026-04-22-13-48 --type change --strict`. Result: passed.
+- [x] 3.4 Run `openspec validate --specs`. Result: passed (`No items found to validate.`).
+
+## 4. Cleanup
+
+- [x] 4.1 Commit the change with a Lore commit message. Result: `d942b84`.
+- [ ] 4.2 Run `gx branch finish --branch agent/codex/setup-current-single-repo-alias-2026-04-22-13-48 --base main --via-pr --wait-for-merge --cleanup`.
+- [ ] 4.3 Record the PR URL and final merge state (`MERGED`) in the completion handoff.
+- [ ] 4.4 Confirm the sandbox worktree and branch refs are gone after cleanup.

src/cli/main.js

@@ -2013,7 +2013,7 @@ function parseRepoTraversalArgs(rawArgs, defaults) {
 
   for (let index = 0; index < rawArgs.length; index += 1) {
     const arg = rawArgs[index];
-    if (arg === '--no-recursive' || arg === '--no-nested' || arg === '--single-repo') {
+    if (arg === '--no-recursive' || arg === '--no-nested' || arg === '--single-repo' || arg === '--current') {
       traversalDefaults.recursive = false;
       continue;
     }
@@ -2088,10 +2088,6 @@ function parseDoctorArgs(rawArgs) {
 
   for (let index = 0; index < rawArgs.length; index += 1) {
     const arg = rawArgs[index];
-    if (arg === '--current') {
-      forwardedArgs.push('--single-repo');
-      continue;
-    }
     if (arg === '--verbose-auto-finish') {
       doctorDefaults.verboseAutoFinish = true;
       continue;
@@ -6689,7 +6685,7 @@ function setup(rawArgs) {
 
   if (discoveredRepos.length > 1) {
     console.log(
-      `[${TOOL_NAME}] Detected ${discoveredRepos.length} git repos under ${topRepoRoot}. Installing into each (use --no-recursive to limit to the top-level).`,
+      `[${TOOL_NAME}] Detected ${discoveredRepos.length} git repos under ${topRepoRoot}. Installing into each (use --no-recursive or --current to limit to the top-level).`,
     );
     for (const repoPath of discoveredRepos) {
       const marker = repoPath === topRepoRoot ? ' (top-level)' : '';

src/context.js

@@ -322,8 +322,8 @@ const SUGGESTIBLE_COMMANDS = [
 ];
 const CLI_COMMAND_DESCRIPTIONS = [
   ['status', 'Show GitGuardex CLI + service health without modifying files'],
-  ['setup', 'Install, repair, and verify guardrails (flags: --repair, --install-only, --target)'],
-  ['doctor', 'Repair drift + verify (auto-sandboxes on protected main)'],
+  ['setup', 'Install, repair, and verify guardrails (flags: --repair, --install-only, --target, --current)'],
+  ['doctor', 'Repair drift + verify (flags: --target, --current; auto-sandboxes on protected main)'],
   ['branch', 'CLI-owned branch workflow surface (start/finish/merge)'],
   ['locks', 'CLI-owned file lock surface (claim/allow-delete/release/status/validate)'],
   ['worktree', 'CLI-owned worktree cleanup surface (prune)'],

test/setup.test.js

@@ -703,6 +703,28 @@ test('setup --no-recursive limits install to the top-level repo', () => {
   );
 });
 
+test('setup --current limits install to the top-level repo', () => {
+  const topDir = initRepo();
+  const nestedA = path.join(topDir, 'apps', 'a');
+  fs.mkdirSync(nestedA, { recursive: true });
+  const initResult = runCmd('git', ['init', '-b', 'dev'], nestedA);
+  assert.equal(initResult.status, 0, initResult.stderr);
+
+  const result = runNode(
+    ['setup', '--target', topDir, '--no-global-install', '--current'],
+    topDir,
+  );
+  assert.equal(result.status, 0, result.stderr || result.stdout);
+  assert.doesNotMatch(result.stdout, /Detected \d+ git repos under/);
+
+  assert.equal(fs.existsSync(path.join(topDir, 'AGENTS.md')), true);
+  assert.equal(
+    fs.existsSync(path.join(nestedA, 'AGENTS.md')),
+    false,
+    'nested repo must not be touched when --current is set',
+  );
+});
+
 
 test('setup refreshes initialized protected main through a sandbox and prunes it', () => {
   const repoDir = initRepoOnBranch('main');