refactor: Major project cleanup and reorganization

## Removed Duplicate Directories
- Deleted old `dashboard/` (replaced by atomizer-dashboard)
- Deleted old `mcp_server/` Python tools (moved model_discovery to optimization_engine)
- Deleted `tests/mcp_server/` (obsolete tests)
- Deleted `launch_dashboard.bat` (old launcher)

## Consolidated Code
- Moved `mcp_server/tools/model_discovery.py` to `optimization_engine/model_discovery/`
- Updated import in `optimization_config_builder.py`
- Deleted stub `extract_mass.py` (use extract_mass_from_bdf instead)
- Deleted unused `intelligent_setup.py` and `hybrid_study_creator.py`
- Archived `result_extractors/` to `archive/deprecated/`

## Documentation Cleanup
- Deleted deprecated `docs/06_PROTOCOLS_DETAILED/` (14 files)
- Archived dated dev docs to `docs/08_ARCHIVE/sessions/`
- Archived old plans to `docs/08_ARCHIVE/plans/`
- Updated `docs/protocols/README.md` with SYS_15

## Skills Consolidation
- Archived redundant study creation skills to `.claude/skills/archive/`
- Kept `core/study-creation-core.md` as canonical

## Housekeeping
- Updated `.gitignore` to prevent `nul` and `_dat_run*.dat`

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

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

docs/protocols/README.md

@@ -64,6 +64,7 @@ Core technical specifications:
 - **SYS_12**: Extractor Library
 - **SYS_13**: Real-Time Dashboard Tracking
 - **SYS_14**: Neural Network Acceleration
+- **SYS_15**: Method Selector
 
 ### Layer 4: Extensions (`extensions/`)
 Guides for extending Atomizer:
@@ -140,6 +141,7 @@ LOAD_WITH: [{dependencies}]
 | 12 | Extractors | [System](system/SYS_12_EXTRACTOR_LIBRARY.md) |
 | 13 | Dashboard | [System](system/SYS_13_DASHBOARD_TRACKING.md) |
 | 14 | Neural | [System](system/SYS_14_NEURAL_ACCELERATION.md) |
+| 15 | Method Selector | [System](system/SYS_15_METHOD_SELECTOR.md) |
 
 ---