| name | deep-audit |
| description | Deep consistency audit of the entire repository infrastructure.
Launches 4 parallel specialist agents to find factual errors, code bugs,
count mismatches, and cross-document inconsistencies. Then fixes all issues
and loops until clean.
Use when: after making broad changes, before releases, or when user says
"audit", "find inconsistencies", "check everything".
|
| author | Claude Code Academic Workflow |
| version | 1.0.0 |
| allowed-tools | ["Read","Write","Edit","Bash","Glob","Grep","Task"] |
/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:
- Read the file first (required by Edit tool)
- Apply the fix
- 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` |
| 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]
