## Review Complete — Principal Systems Engineer (Google/Stripe caliber), Round 3

### Perspective
Distributed systems, API design, reliability, observability. What happens when this fails at 3am? Where are the race conditions? Is the API surface minimal and composable? Can I debug a broken run from the logs alone? What's the blast radius of a bad agent session?

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### Completeness Assessment

All 19 functional requirements are implemented and verified:

| FR | Status | Evidence |
|----|--------|----------|
| FR-1: `git ls-files` with timeout | ✅ | `get_tracked_files()` — 30s timeout, OSError/TimeoutExpired caught |
| FR-2: Python AST extraction | ✅ | `extract_python_symbols()` — docstrings, classes w/ bases, methods, functions |
| FR-3: JS/TS regex extraction | ✅ | `extract_js_ts_symbols()` — 6 regex patterns for exports, classes, interfaces, types |
| FR-4: Other files → path + size | ✅ | `extract_other_file_info()` |
| FR-5: Tree-formatted output | ✅ | `format_tree()` with directory grouping and indentation |
| FR-6: Sensitive file denylist | ✅ | `SENSITIVE_PATTERNS` tuple, hardcoded, applied before user config |
| FR-7: Token estimation chars/4 | ✅ | `truncate_to_budget()` uses `max_chars = max_tokens * 4` |
| FR-8: Relevance ranking | ✅ | `rank_by_relevance()` — keyword overlap with tiered scoring |
| FR-9: Exact path/basename match | ✅ | 1000.0/500.0 score boosts in `_score()` |
| FR-10: Overview always included | ✅ | `generate_overview()` + unconditional inclusion in `truncate_to_budget()` |
| FR-11: File count cap | ✅ | `config.max_files` applied in `get_tracked_files()` with warning log |
| FR-12: `RepoMapConfig` dataclass | ✅ | 5 fields matching spec exactly |
| FR-13: `ColonyConfig.repo_map` field | ✅ | Field added with `field(default_factory=RepoMapConfig)` |
| FR-14: Config parsing + serialization | ✅ | `_parse_repo_map_config()` + `save_config()` with defaults-only-if-changed |
| FR-15: All pipeline phases injected | ✅ | Plan, Implement (seq+parallel), Review, Fix, Decision, Deliver, CEO — all 8 |
| FR-16: Programmatic injection | ✅ | `_inject_repo_map()` appends to system prompt, same pattern as `_inject_memory_block()` |
| FR-17: Skip when disabled | ✅ | `config.repo_map.enabled` checked in `_run_pipeline()` and `run_ceo()` |
| FR-18: `## Repository Structure` header | ✅ | Exact format in `_inject_repo_map()` |
| FR-19: CLI `colonyos map` command | ✅ | `--max-tokens` and `--prompt` flags, loads config, prints to stdout |

### Quality Assessment

**No TODOs, FIXMEs, or placeholder code.** Zero linter issues in the diff. All 660 tests pass.

### Reliability & Failure Modes

1. **Fail-closed at every layer.** `generate_repo_map()` is wrapped in `try/except Exception` in both `_run_pipeline()` and `run_ceo()`. A crash in map generation produces a warning log and the pipeline continues with `repo_map_text = ""`. This is exactly the right design — the map is a nice-to-have context enhancement, not a load-bearing dependency.

2. **Subprocess timeout is bounded.** `git ls-files` has a 30s timeout. `TimeoutExpired` is caught and returns `[]`. No unbounded subprocess calls.

3. **File size guard prevents OOM.** `_MAX_PARSE_SIZE = 1MB` prevents `read_text()` on generated megafiles. Both Python and JS/TS extractors check `stat().st_size` before reading.

4. **No race conditions.** The map is generated once, stored as a string, and passed by value to all phases. No mutable shared state. No file locks needed. No cache invalidation problem because there's no cache — per-run only.

5. **Logging is sufficient for 3am debugging.** Warning on `git ls-files` failure, warning on file count cap, info on parse skips, and the `_log()` call in `_inject_repo_map()` showing char count. If a map injection fails, the pipeline log will show why.

### Non-blocking Findings

1. **[src/colonyos/cli.py:1283]**: `type(repo_map_config)(...)` works but is fragile — if `RepoMapConfig` is ever subclassed or `type()` is overridden, this breaks silently. `dataclasses.replace(repo_map_config, max_tokens=max_tokens)` is idiomatic Python and does the same thing in one line. Cosmetic.

2. **[src/colonyos/repo_map.py:27-28]**: Duplicated comment `# Hardcoded sensitive file patterns that are always excluded (FR-6).` appears twice (lines 27 and 31). The first instance is a leftover from when `_MAX_PARSE_SIZE` was added between them. Cosmetic.

3. **[src/colonyos/repo_map.py:rank_by_relevance]**: The scoring function is O(files × keywords × symbols). For a 2000-file repo with a verbose prompt, this could produce a noticeable pause, but it's bounded by `max_files` and the keyword extraction is simple splitting, so worst case is ~100ms. Acceptable for V1.

4. **[src/colonyos/orchestrator.py:2234-2242]**: The CEO phase generates its own `repo_map_text` via a fresh `generate_repo_map()` call, while all other phases share the one generated at pipeline start. This is correct behavior (CEO is called independently) but means a CEO-only invocation pays the full map generation cost. Not a problem, just worth noting.

### Safety

- ✅ No secrets or credentials in committed code
- ✅ Sensitive file denylist is hardcoded before user config (cannot be overridden)
- ✅ No destructive operations — module only reads files and runs `git ls-files`
- ✅ `ast.parse()` is used for analysis only, never `eval()` or `exec()`
- ✅ No `shell=True` in subprocess calls

### Test Coverage

- **95 repo_map tests** — comprehensive coverage including git integration tests with real `git init`, AST extraction, JS/TS regex, tree formatting, relevance ranking, truncation, and size guard tests
- **103 config tests** — parse/serialize round-trip, validation (negative values rejected), defaults
- **65 CLI tests** — `colonyos map` with `--max-tokens`, `--prompt`, empty repo
- **154 orchestrator tests** — injection into all 8 phases, disabled config skips, error resilience
- **660 total, 0 failures**

---

VERDICT: approve

FINDINGS:
- [src/colonyos/cli.py:1283]: `type(repo_map_config)(...)` should be `dataclasses.replace()` — fragile if class is ever subclassed, cosmetic
- [src/colonyos/repo_map.py:27-28]: Duplicated comment "Hardcoded sensitive file patterns..." appears twice, leftover from _MAX_PARSE_SIZE insertion, cosmetic
- [src/colonyos/repo_map.py:rank_by_relevance]: O(files × keywords × symbols) scoring is fine under the 2000-file cap but worth noting for future profiling

SYNTHESIS:
This is a clean, well-architected module that follows every existing codebase convention exactly. The key reliability decision — fail-closed with `try/except Exception` around map generation so it can never crash the pipeline — is the right call. The module has zero mutable shared state, zero new dependencies, bounded subprocess calls, bounded file reads, and a linear pipeline that is trivially debuggable from logs. All 19 PRD requirements are implemented and verified by 660 passing tests with real git integration. The three non-blocking findings are purely cosmetic. From a systems reliability perspective, the blast radius of any failure in this module is zero — the pipeline continues without a map, logs a warning, and the operator can diagnose from the run log. Ship it.
