- Add src/splicing/ module with scaffold_prep, fragment_prep, and engine
- Add tylosin_splicer.py entry script
- Add unit tests for splicing components
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add AGENTS.md with AI assistant guidelines for the project
- Add tests/test_ring_numbering.py to verify ring numbering consistency
- Test confirms atom numbering is fixed and reproducible
Co-Authored-By: Claude <noreply@anthropic.com>
