docs

Check that all code has appropriate documentation.

Arguments: $ARGUMENTS (optional scope)

• commit: Check only staged files
• pr: Check all files changed in the current PR
• all: Check the entire codebase
• If no argument provided:
  • If in a PR branch: defaults to ‘pr’
  • Otherwise: defaults to ‘commit’

Phase 1: Scope Determination

1. Determine scope based on $ARGUMENTS

Phase 2: Documentation Analysis

2. Identify functions/classes lacking documentation
3. Check quality of existing documentation
4. Extract project documentation standards from CLAUDE.md

Phase 3: Documentation Updates

3. For identified gaps:

   • Generate documentation following project conventions
   • Apply language-specific formats (roxygen2, docstrings, JSDoc)
   • Use @inheritParams in R to avoid duplication

4. For R projects: Run devtools::document() to update man/ files

Phase 4: Quality Verification

5. Verify documentation format compliance and no broken references

Phase 5: Report Results

6. Summary of files checked, documentation added/updated, and remaining issues

Auto-Exit When Standalone

IMPORTANT: If this command is being run as a standalone request, automatically exit after completing all phases successfully.