fix: detect .git-only stale workdir; wire run_external repo cloning

[wwind123]

Summary

• _is_stale_default_workdir extended (config.py): previously returned False as soon as .git/ existed, so a workdir with .git/ but no source files (e.g. after accidental wipe leaving only response storage at .git/agent-loop/) was never detected as stale. Now also flags the case where .git is present but the working tree contains no non-artifact files.

• run_external.py now validates/re-clones the workdir (run_external.py, skill_runner.py): run_external was being called with --workdir but never called ensure_temp_checkout, so it would fail silently if the workdir was absent or stale. Added --repo OWNER/REPO; when provided, run_external calls ensure_temp_checkout with the real repo before launching the agent. skill_runner now passes --repo on every run_external invocation.

• Fixed a misleading comment in skill_runner.py that claimed cloning was handled by --workdir (it wasn't).

Test plan

• tests/test_agent_loop.py -k stale — three tests, including new test_stale_default_workdir_git_only_is_recreated
• tests/test_skill_helpers.py — 22 tests unchanged

🤖 Generated with Claude Code

-- Anthropic Claude

[wwind123]

Review verdict: Blocking

The PR correctly extends stale workdir detection to handle .git-only directories and wires up repository cloning in run_external.py. However, it fails to handle completely empty directories as stale, which causes skill_runner.py to fail on first run because it pre-creates the workdir.

Blocking issues

• _is_stale_default_workdir in src/coding_review_agent_loop/config.py still requires the directory to be non-empty (via bool(contents)) to be considered stale in the non-git case. This blocks auto-cloning when helpers/skill_runner.py creates an empty directory before calling run_external.py, as ensure_temp_checkout will find the directory exists but is not stale, skipping the clone and failing later with a 'not a git checkout' error.

Same-PR follow-ups

• Import AgentName in helpers/run_external.py and remove the type: ignore[arg-type] on the ensure_temp_checkout call to maintain type safety.

-- Google Gemini

[wwind123]

Change summary (round 1 feedback)

Gemini blocking item (real bug, fixed): _is_stale_default_workdir required bool(contents) to be true in the no-.git branch, so an empty directory was never flagged as stale. When ensure_temp_checkout found an empty-but-existing Codex workdir, it skipped the clone and crashed in _sync_base_branch. Fixed by removing the bool(contents) guard — an empty directory with no git checkout is always stale.

Gemini same-PR followup (fixed): run_external.py now declares agent_name: AgentName (cast from the argparse string, which is always valid) and removes all three type: ignore[arg-type] annotations.

Added test_stale_default_workdir_empty_is_recreated covering the empty-dir case. All 4 stale workdir tests pass.

-- Anthropic Claude

[wwind123]

Review verdict: Approved

The PR successfully addresses the prior review items and improves the robustness of workdir management in run_external. _is_stale_default_workdir now correctly identifies empty or .git-only directories as stale, triggering a re-clone when necessary. The addition of --repo to run_external ensures that it can autonomously manage the checkout state. Type safety is also improved by properly importing and using AgentName.

Prior unresolved item dispositions

• [item-1] Blocking issue from Google Gemini, round 1: _is_stale_default_workdir in src/coding_review_agent_loop/config.py still requires the direct... -> resolved
• [item-2] Same-PR follow-up from Google Gemini, round 1: Import AgentName in helpers/run_external.py and remove the type: ignore[arg-type] on the `e... -> resolved

-- Google Gemini

[wwind123]

Review verdict: Approved

Approved. The stale workdir detection now covers empty and .git-only default workdirs, and run_external is wired to validate or re-clone when skill_runner supplies the repo.

Prior unresolved item dispositions

• [item-1] Blocking issue from Google Gemini, round 1: _is_stale_default_workdir in src/coding_review_agent_loop/config.py still requires the direct... -> resolved
• [item-2] Same-PR follow-up from Google Gemini, round 1: Import AgentName in helpers/run_external.py and remove the type: ignore[arg-type] on the `e... -> resolved

-- OpenAI Codex