- Move lsp-integration.md and secure-console-v3.md to docs/archive-obsolete/
(these features are now in the Nextra SaaS product)
- Update CLAUDE.md with current project state
- Simplify run_organism.py
- Fix test fixtures for shared backend compatibility
- Minor handler and llm_api cleanups
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>