docs: add comprehensive Phase 2 documentation and mark completion
Created detailed user guide for schema refinement tools:
- Command reference for schema-analyze and schema-refine
- Complete options and examples
- Issue type explanations with before/after examples
- Workflow guides (basic, interactive, CI/CD, migration)
- Best practices and troubleshooting
- Integration examples (Git hooks, Makefile, Python)
- Rigidity score interpretation table
Updated TODO.md to mark Phase 2 completion:
- Documented all delivered features
- Listed key capabilities (rigidity detection, auto-refine, interactive mode)
- Noted test coverage (33 tests, 100% passing)
- Added example results (60/100 → 24/100 rigidity reduction)
Phase 2 is now complete and fully documented.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
tegwick
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