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documentation-audit

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Full audit and update of BioETL project documentation for v5.22+. Use when asked to review docs for staleness, reconcile docs with code, sync RULES.md and REQUIREMENTS.md, update architecture/provider/contract docs, reflect ADR-010/ADR-014/ADR-017, or identify dead documentation.

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Source SKILL.md: https://github.com/majiayu000/claude-skill-registry/blob/HEAD/skills/documents/skills-satorykono-bioactivitydataacqui/SKILL.md

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Documentation Audit

Objective

Perform a full documentation audit of BioETL and bring docs in sync with code and ADRs (v5.22+). Produce a clear audit report, a prioritized plan, and updated documentation changes.

Required inputs (before starting)

  • Load .claude/skills/documentation-audit.audit-checklist.md — checklist for each audit area.
  • Load .claude/skills/documentation-audit.report-template.md — template for the audit report.

Workflow

1. Intake and scope

  • Confirm repo root and target version (v5.22+).
  • Identify doc entry points: README.md, mkdocs.yml.
  • List files under docs/: rg --files docs.

2. Audit (follow audit-checklist.md)

  • Compare documentation to current code and configs.
  • Focus: RULES.md, REQUIREMENTS.md, architecture, provider, contract docs.
  • Check ADR alignment: ADR-010 (Local-Only), ADR-014 (Determinism), ADR-017 (Observability).
  • Record findings with severity: Critical, High, Medium, Low.

3. Plan

  • Turn findings into a concrete change list.
  • Prioritize by impact (Critical > High > Medium > Low).
  • Call out unknowns that need user confirmation.

4. Update (if user requests)

  • Edit docs to match current code and ADRs.
  • Keep versions and dates explicit in text.
  • For obsolete docs: propose delete/archive, do not remove unless user asks.

5. Verify

  • Check links and nav entries (mkdocs.yml).
  • Confirm RULES.md and REQUIREMENTS.md are synchronized.
  • Ensure ADRs are reflected in top-level docs.

Practical commands

# ADR references
rg -n "ADR-010|ADR-014|ADR-017" docs README.md mkdocs.yml

# Version mentions
rg -n "v5\.14|5\.14" docs README.md

# Doc refs in nav
rg -n "docs/|\.md" mkdocs.yml README.md

# Orphan scan: list docs/ then search each filename in mkdocs.yml and other docs
rg --files docs

Output format

  • Use .claude/skills/documentation-audit.report-template.md structure for the audit report.
  • Provide a short prioritized change list and required user decisions.
  • Do not change code unless explicitly requested; focus on documentation.

Constraints

MUST

  • Use .claude/skills/documentation-audit.report-template.md for the audit report.
  • Verify findings against actual code and configs.
  • Record severity for each finding.

MUST NOT

  • Change code unless user explicitly asks.
  • Remove docs without explicit user approval.
  • Document desired behavior instead of reality when code and docs diverge — flag and propose options.

SHOULD

  • Prefer documenting reality; when code and docs diverge, flag and propose options.