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>

optimization_engine/extractors/extract_mass.py

@@ -1,39 +0,0 @@
-"""
-Extract total structural mass
-Auto-generated by Atomizer Phase 3 - pyNastran Research Agent
-
-Pattern: generic_extraction
-Element Type: General
-Result Type: unknown
-API: model.<result_type>[subcase]
-"""
-
-from pathlib import Path
-from typing import Dict, Any
-import numpy as np
-from pyNastran.op2.op2 import OP2
-
-
-def extract_generic(op2_file: Path):
-    """Generic OP2 extraction - needs customization."""
-    from pyNastran.op2.op2 import OP2
-
-    model = OP2()
-    model.read_op2(str(op2_file))
-
-    # TODO: Customize extraction based on requirements
-    # Available: model.displacements, model.ctetra_stress, etc.
-    # Use model.get_op2_stats() to see available results
-
-    return {'result': None}
-
-
-if __name__ == '__main__':
-    # Example usage
-    import sys
-    if len(sys.argv) > 1:
-        op2_file = Path(sys.argv[1])
-        result = extract_generic(op2_file)
-        print(f"Extraction result: {result}")
-    else:
-        print("Usage: python {sys.argv[0]} <op2_file>")