# Review by Principal Systems Engineer (Google/Stripe caliber) (Round 2)

I've completed a thorough review of the implementation. Here is my assessment:

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## Review: Principal Systems Engineer Perspective

### Completeness Check

All functional requirements from the PRD are implemented:
- **FR-1/2**: `cleanup` command group with `branches`, `artifacts`, `scan` subcommands ✅
- **FR-3–10**: Branch cleanup with merged detection, prefix filtering, `--all-branches`, `--include-remote`, `--execute`, current/default branch protection, open PR check, summary ✅
- **FR-11–16**: Artifact cleanup with retention, dry-run, `--retention-days`, RUNNING protection, summary ✅
- **FR-17–21**: Structural scan with static analysis, thresholds, `--ai` flag, report output, `--refactor` delegation ✅
- **FR-22–23**: `CleanupConfig` dataclass wired into `ColonyConfig`, CLI flags override ✅
- **FR-24–27**: Audit logging, cleanup log self-protection, AI constraints in `cleanup_scan.md` ✅

### Tests

All **1,087 tests pass** (57 cleanup-specific + 112 CLI tests including new cleanup commands). No regressions.

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VERDICT: approve

FINDINGS:
- [src/colonyos/cleanup.py:197-208]: `check_branch_safety` calls `check_open_pr` with a 5-second timeout per branch, executed sequentially. With 50+ stale branches this becomes a 4+ minute wall-clock operation. Consider batching via a single `gh pr list` query or parallelizing with `concurrent.futures`. Not a blocker for v1 but will become painful at scale.
- [src/colonyos/cleanup.py:526-528]: `write_cleanup_log` uses second-granularity timestamps (`%Y%m%d_%H%M%S`). Two cleanup operations in the same second silently overwrite each other's audit log. Adding a short random suffix or using microseconds would eliminate this.
- [src/colonyos/cli.py:2215-2222]: Branch results table shows empty string for `Last Commit` on branches marked for deletion — the data is available on `BranchInfo` but not looked up from the input list. Minor UX gap.
- [src/colonyos/cli.py:2394-2420]: AI scan reuses `Phase.REVIEW` which is semantically incorrect (this is analysis, not a review). Works today but could cause confusion in metrics/logging. Consider adding a `Phase.SCAN` or using a dedicated phase string.
- [src/colonyos/cleanup.py:267-270]: In dry-run mode, branches are added to `deleted_local` without running `check_branch_safety` — wait, they are checked. Actually re-reading: safety check happens at line 253 before the execute/dry-run branch. Correct. ✓
- [src/colonyos/cleanup.py:275]: Uses `git branch -d` (lowercase) which refuses to delete unmerged branches — this is the correct fail-safe choice over `-D`. Good defense-in-depth against TOCTOU between listing and deleting.
- [src/colonyos/cleanup.py:347-349]: `list_stale_artifacts` skips `cleanup_*` files — satisfies FR-25 (cleanup logs can't be deleted by cleanup). Clean implementation.
- [src/colonyos/instructions/cleanup_scan.md:9]: Explicitly forbids touching auth/secrets/sanitization files per FR-27. ✅

SYNTHESIS:
This is a clean, well-structured implementation that follows the established project patterns (`doctor.py` module pattern, lazy imports, Rich tables). The critical safety invariants are all met: dry-run by default, `--execute` required for destruction, current/default branch protection, open PR checks with fail-closed semantics, and `git branch -d` (not `-D`) as defense-in-depth. The audit logging covers all three subcommands. The two concerns I'd prioritize for follow-up are (1) the sequential PR-check latency for branch cleanup at scale, and (2) the timestamp collision risk in audit log filenames — both are operational reliability issues that won't bite in v1 but will surface as adoption grows. The code is well-tested (57 dedicated unit tests), handles errors gracefully, and the AI scan pathway correctly inherits base instruction constraints. No secrets in code, no destructive operations without safeguards. Approved for merge.