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>

.claude/skills/archive/create-study.md

@@ -0,0 +1,30 @@
+# Create Study Skill - REDIRECT
+
+**DEPRECATED**: This file has been consolidated.
+
+---
+
+## Use Instead
+
+For study creation, use the core skill:
+
+```
+.claude/skills/core/study-creation-core.md
+```
+
+## Why This Changed
+
+Phase 3 of the Agentic Architecture consolidated duplicate skills:
+- This file (2207 lines) duplicated content from `core/study-creation-core.md` (739 lines)
+- The core version is more focused and maintainable
+- All extractor references now point to `SYS_12_EXTRACTOR_LIBRARY.md`
+
+## Migration
+
+If you were loading `create-study.md`, now load:
+1. `core/study-creation-core.md` - Core study creation logic
+2. `SYS_12_EXTRACTOR_LIBRARY.md` - Extractor reference (single source of truth)
+
+---
+
+*Consolidated: 2025-12-07 | Phase 3: Skill Consolidation*