feat: Pre-migration checkpoint - updated docs and utilities

Updates before optimization_engine migration:
- Updated migration plan to v2.1 with complete file inventory
- Added OP_07 disk optimization protocol
- Added SYS_16 self-aware turbo protocol
- Added study archiver and cleanup utilities
- Added ensemble surrogate module
- Updated NX solver and session manager
- Updated zernike HTML generator
- Added context engineering plan
- LAC session insights updates

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

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

CLAUDE.md

@@ -90,6 +90,7 @@ The Protocol Operating System (POS) provides layered documentation:
 | Analyze results | OP_04 | `docs/protocols/operations/OP_04_ANALYZE_RESULTS.md` |
 | Export neural data | OP_05 | `docs/protocols/operations/OP_05_EXPORT_TRAINING_DATA.md` |
 | Debug issues | OP_06 | `docs/protocols/operations/OP_06_TROUBLESHOOT.md` |
+| **Free disk space** | OP_07 | `docs/protocols/operations/OP_07_DISK_OPTIMIZATION.md` |
 
 ## System Protocols (Technical Specs)
 
@@ -135,14 +136,15 @@ C:\Users\antoi\anaconda3\envs\atomizer\python.exe your_script.py
 Atomizer/
 ├── .claude/skills/           # LLM skills (Bootstrap + Core + Modules)
 ├── docs/protocols/           # Protocol Operating System
-│   ├── operations/           # OP_01 - OP_06
+│   ├── operations/           # OP_01 - OP_07
 │   ├── system/              # SYS_10 - SYS_15
 │   └── extensions/          # EXT_01 - EXT_04
 ├── optimization_engine/     # Core Python modules
 │   ├── extractors/          # Physics extraction library
 │   ├── gnn/                 # GNN surrogate module (Zernike)
-│   └── utils/               # Utilities (dashboard_db, trial_manager)
+│   └── utils/               # Utilities (dashboard_db, trial_manager, study_archiver)
 ├── studies/                 # User studies
+├── tools/                   # CLI tools (archive_study.bat, zernike_html_generator.py)
 ├── archive/                 # Deprecated code (for reference)
 └── atomizer-dashboard/      # React dashboard
 ```