Anto01 69c0d76b50 docs: Mark restructuring plan as complete ...

All phases successfully implemented:
- OP_08 report generation added
- Protocol numbering fixed (SYS_16-18)
- Code reorganized (surrogates, tests)
- Dependencies cleaned (pyproject.toml)
- M1_Mirror studies archived
- README updated with LLM section

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

2026-01-07 09:09:22 -05:00

..

04_USER_GUIDES

feat: Add Analysis page, run comparison, notifications, and config editor

2025-12-05 19:57:20 -05:00

05_API_REFERENCE

feat: Major update with validators, skills, dashboard, and docs reorganization

2025-11-25 19:23:58 -05:00

06_PHYSICS

docs: Consolidate documentation and fix protocol numbering (partial)

2026-01-07 08:52:07 -05:00

07_DEVELOPMENT

refactor: Major project cleanup and reorganization

2025-12-12 11:24:02 -05:00

08_ARCHIVE

refactor: Major project cleanup and reorganization

2025-12-12 11:24:02 -05:00

09_DIAGRAMS

feat: Major update with validators, skills, dashboard, and docs reorganization

2025-11-25 19:23:58 -05:00

api

docs: Consolidate documentation and fix protocol numbering (partial)

2026-01-07 08:52:07 -05:00

generated

feat: Implement Agentic Architecture for robust session workflows

2025-12-07 14:52:25 -05:00

guides

feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools

2025-12-23 19:47:37 -05:00

plans

docs: Mark restructuring plan as complete

2026-01-07 09:09:22 -05:00

protocols

docs: Consolidate documentation and fix protocol numbering (partial)

2026-01-07 08:52:07 -05:00

00_INDEX.md

feat: Major update with validators, skills, dashboard, and docs reorganization

2025-11-25 19:23:58 -05:00

01_PROTOCOLS.md

feat: Major update with validators, skills, dashboard, and docs reorganization

2025-11-25 19:23:58 -05:00

02_ARCHITECTURE.md

feat: Major update with validators, skills, dashboard, and docs reorganization

2025-11-25 19:23:58 -05:00

03_GETTING_STARTED.md

feat: Major update with validators, skills, dashboard, and docs reorganization

2025-11-25 19:23:58 -05:00

ATOMIZER_PODCAST_BRIEFING.md

feat: Implement Study Interview Mode as default study creation method

2026-01-03 11:06:07 -05:00

CONTEXT_ENGINEERING_REPORT.md

feat: Implement ACE Context Engineering framework (SYS_17)

2025-12-29 20:21:20 -05:00

TODO_NXOPEN_MCP_SETUP.md

feat: Pre-migration checkpoint - updated docs and utilities

2025-12-29 10:22:45 -05:00