brycewang-stanford/deep-audit

/deep-audit — Repository Infrastructure Audit

Run a comprehensive consistency audit across the entire repository, fix all issues found, and loop until clean.

When to Use

• After broad changes (new skills, rules, hooks, guide edits)
• Before releases or major commits
• When the user asks to "find inconsistencies", "audit", or "check everything"

Workflow

PHASE 1: Launch 4 Parallel Audit Agents

Launch these 4 agents simultaneously using Task with subagent_type=general-purpose:

Agent 1: Guide Content Accuracy

Focus: guide/workflow-guide.qmd

• All numeric claims match reality (skill count, agent count, rule count, hook count)
• All file paths mentioned actually exist on disk
• All skill/agent/rule names match actual directory names
• Code examples are syntactically correct
• Cross-references and anchors resolve
• No stale counts from previous versions

Agent 2: Hook Code Quality

Focus: .claude/hooks/*.py and .claude/hooks/*.sh

• No remaining /tmp/ usage (should use ~/.claude/sessions/)
• Hash length consistency ([:8] across all hooks)
• Proper error handling (fail-open pattern: top-level try/except with sys.exit(0))
• JSON input/output correctness (stdin for input, stdout/stderr for output)
• Exit code correctness (0 for non-blocking, non-zero only when intentionally blocking)
• from __future__ import annotations for Python 3.8+ compatibility
• Correct field names from hook input schema (source not type for SessionStart)
• PreCompact hooks print to stderr (stdout is ignored)

Agent 3: Skills and Rules Consistency

Focus: .claude/skills/*/SKILL.md and .claude/rules/*.md

• Valid YAML frontmatter in all files
• No stale disable-model-invocation: true
• allowed-tools values are sensible
• Rule paths: reference existing directories
• No contradictions between rules
• CLAUDE.md skills table matches actual skill directories 1:1
• All templates referenced in rules/guide exist in templates/

Agent 4: Cross-Document Consistency

Focus: README.md, docs/index.html, docs/workflow-guide.html

• All feature counts agree across all 3 documents
• All links point to valid targets
• License section matches LICENSE file
• Directory tree matches actual structure
• No stale counts from previous versions

PHASE 2: Triage Findings

Categorize each finding:

• Genuine bug: Fix immediately
• False alarm: Discard (document WHY it's false for future rounds)

Common false alarms to watch for:

• Quarto callout ## Title inside ::: divs — this is standard syntax, NOT a heading bug
• allowed-tools linter warning — known linter bug (Claude Code issue #25380), field IS valid
• Counts in old session logs — these are historical records, not user-facing docs

PHASE 3: Fix All Issues

Apply fixes in parallel where possible. For each fix:

1. Read the file first (required by Edit tool)
2. Apply the fix
3. Verify the fix (grep for stale values, check syntax)

PHASE 4: Re-render if Guide Changed

If guide/workflow-guide.qmd was modified:

quarto render guide/workflow-guide.qmd
cp guide/workflow-guide.html docs/workflow-guide.html

PHASE 5: Loop or Declare Clean

After fixing, launch a fresh set of 4 agents to verify.

• If new issues found → fix and loop again
• If zero genuine issues → declare clean and report summary

Max loops: 5 (to prevent infinite cycling)

Key Lessons from Past Audits

These are real bugs found across 7 rounds — check for these specifically:

| Bug Pattern | Where to Check | What Went Wrong | |-------------|---------------|-----------------| | Stale counts ("19 skills" → "21") | Guide, README, landing page | Added skills but didn't update all mentions | | Hook exit codes | All Python hooks | Exit 2 in PreCompact silently discards stdout | | Hook field names | post-compact-restore.py | SessionStart uses source, not type | | State in /tmp/ | All Python hooks | Should use ~/.claude/sessions/<hash>/ | | Hash length mismatch | All Python hooks | Some used [:12], others [:8] | | Missing fail-open | Python hooks __main__ | Unhandled exception → exit 1 → confusing behavior | | Python 3.10+ syntax | Type hints like dict | None | Need from __future__ import annotations | | Missing directories | quality_reports/specs/ | Referenced in rules but never created | | Always-on rule listing | Guide + README | meta-governance omitted from listings | | macOS-only commands | Skills, rules | open without xdg-open fallback | | Protected file blocking | settings.json edits | protect-files.sh blocks Edit/Write |

Output Format

After each round, report:

## Round N Audit Results

### Issues Found: X genuine, Y false alarms

| # | Severity | File | Issue | Status |
|---|----------|------|-------|--------|
| 1 | Critical | file.py:42 | Description | Fixed |
| 2 | Medium | file.qmd:100 | Description | Fixed |

### Verification
- [ ] No stale counts (grep confirms)
- [ ] All hooks have fail-open + future annotations
- [ ] Guide renders successfully
- [ ] docs/ updated

### Result: [CLEAN | N issues remaining]