# Review by Staff Security Engineer (Round 2)

I now have a comprehensive view of the implementation. Here's my review:

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## Staff Security Engineer Review

### Completeness Assessment

All PRD functional requirements (FR-1 through FR-27) are implemented:
- ✅ CLI structure with `cleanup` group and three subcommands (FR-1, FR-2)
- ✅ Branch cleanup with prefix filtering, dry-run, `--execute`, `--include-remote`, open PR checks (FR-3 through FR-10)
- ✅ Artifact cleanup with retention, dry-run, `--execute`, RUNNING protection (FR-11 through FR-16)
- ✅ Structural scan with static analysis, thresholds, categories (FR-17, FR-18)
- ✅ AI scan with `--ai` flag using instruction template (FR-19, FR-20)
- ✅ `--refactor` delegation to `colonyos run` pipeline (FR-21)
- ✅ `CleanupConfig` with all fields wired into `ColonyConfig` (FR-22, FR-23)
- ✅ Audit logging to `cleanup_<timestamp>.json` (FR-24)
- ✅ Cleanup logs are skipped by artifact cleanup (FR-25)
- ✅ AI scan inherits base.md constraints and explicitly forbids auth/security file modifications (FR-26, FR-27)
- All 57 unit tests pass, all 112 CLI tests pass, all tasks marked complete.

### Security Findings

VERDICT: approve

FINDINGS:
- [src/colonyos/cleanup.py:220-228]: **Good: Fail-closed PR check.** When `check_open_pr` raises any exception, the branch is skipped with "unable to verify PR status." This is the correct security posture — network failures default to safety, not deletion.
- [src/colonyos/cleanup.py:275]: **Good: Uses `git branch -d` (not `-D`).** The lowercase `-d` flag refuses to delete branches not fully merged, providing a second layer of protection against data loss even if the `--merged` filter has edge cases.
- [src/colonyos/cleanup.py:335-336]: **Good: Cleanup logs are self-protecting.** `list_stale_artifacts` explicitly skips files prefixed with `cleanup_`, satisfying FR-25 that cleanup cannot delete its own audit trail.
- [src/colonyos/cli.py:2460]: **Good: AI scan tool allowlist is read-only.** `allowed_tools=["Read", "Glob", "Grep", "Agent"]` — no Write, Edit, or Bash. The AI scan cannot modify files or execute arbitrary commands, which is the critical safety boundary.
- [src/colonyos/instructions/cleanup_scan.md:8-9]: **Good: Explicit constraints in instruction template.** "DO NOT modify any files", "DO NOT create any commits", "DO NOT touch files related to authentication, authorization, secrets, or input sanitization." These are defense-in-depth constraints alongside the tool allowlist.
- [src/colonyos/cleanup.py]: **Good: No `shell=True`, no `os.system`, no `eval/exec`.** All subprocess calls use list-form arguments, preventing shell injection via branch names or paths.
- [src/colonyos/cleanup.py:178-183]: **Good: Default/current branch protection.** Hardcoded exclusion of the default branch and current branch from deletion candidates, not just in the safety check but also in the listing function itself.
- [src/colonyos/cli.py:2186-2190]: **Good: Dry-run default across all destructive operations.** `--execute` is an opt-in flag, not a `--dry-run` opt-out, matching the PRD's zero-risk-by-default philosophy.
- [src/colonyos/cleanup.py:331-332]: **Minor observation:** `list_stale_artifacts` reads arbitrary JSON from `.colonyos/runs/`. If an attacker could plant a malicious JSON file there (e.g., via a PR that modifies that directory), the `json.loads` would parse it but the data is only used for display (run_id, status, started_at) — no deserialization of executable objects, no `eval`. Low risk.
- [src/colonyos/cli.py:2443-2462]: **Observation: AI scan uses `Phase.REVIEW` phase.** This means it inherits the REVIEW phase's model and budget, which is appropriate for an analysis-only task. The budget is bounded by `config.budget.per_phase`.

SYNTHESIS:
This is a well-designed implementation from a security perspective. The critical design decisions are sound: destructive operations default to dry-run with explicit `--execute` opt-in, branch deletion is fail-closed (skip on any uncertainty), the AI scan has a strict read-only tool allowlist that prevents code modification, and all subprocess calls use list-form arguments preventing shell injection. The audit trail is self-protecting — cleanup logs cannot be deleted by the cleanup command itself. The `--refactor` path correctly delegates through the full `colonyos run` pipeline with all review gates intact, rather than performing autonomous code changes. The only area I'd note for future hardening is that the instruction template constraints ("DO NOT modify files") are soft guardrails — but they're backed by the hard guardrail of the read-only tool allowlist, making this defense-in-depth rather than relying solely on prompt compliance. Overall, this implementation demonstrates a strong security posture appropriate for a tool that operates in users' repositories.