- Add scripts/consistency_audit.py with 4 automated checks
- Check 1: No old command names in active code/docs
- Check 2: No paperforge_lite references in Python code
- Check 3: No dead internal links in markdown
- Check 4: Command docs have required sections
Fix violations found by audit:
- Update paperforge/ocr_diagnostics.py error messages to use new commands
- Update pipeline/worker/literature_pipeline.py generated content to use /pf-deep
- Update scripts/welcome.py to recommend /pf-deep
- Update skills/literature-qa/prompt_deep_subagent.md title to /pf-deep
- Update skills/literature-qa/scripts/ld_deep.py docstrings to /pf-deep
- Fix dead links in docs/COMMANDS.md and command/*.md
- Update AGENTS.md migration section to reference MIGRATION-v1.2.md
- Update paperforge/cli.py module docstring to use current commands
- Standardize all 5 command docs with unified template:
Purpose, CLI Equivalent, Prerequisites, Arguments,
Example, Output, Error Handling, Platform Notes, See Also
- Preserve all existing functional content
- Add platform notes for OpenCode/Codex/Claude Code
- Add cross-references to AGENTS.md and COMMANDS.md
- Convert ocr parser to sub-subcommands (run, doctor)
- Add _cmd_ocr_doctor() with formatted tiered report output
- Update dispatch logic to route ocr doctor subcommand
- Add CLI dispatch test for doctor command
- Update command/lp-ocr.md with doctor documentation
