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>

archive/deprecated/result_extractors/generated/extract_solid_stress.py

@@ -0,0 +1,127 @@
+"""
+Extract von Mises stress from solid and shell elements
+Auto-generated by Atomizer Phase 3 - pyNastran Research Agent
+
+Pattern: element_stress
+Element Types: CTETRA, CHEXA, CPENTA (solids), CQUAD4, CTRIA3 (shells)
+Result Type: stress
+API: model.ctetra_stress[subcase], model.cquad4_stress[subcase], etc.
+"""
+
+from pathlib import Path
+from typing import Dict, Any
+import numpy as np
+from pyNastran.op2.op2 import OP2
+
+
+def extract_solid_stress(op2_file: Path, subcase: int = 1, element_type: str = 'auto'):
+    """
+    Extract stress from solid or shell elements.
+
+    Args:
+        op2_file: Path to OP2 file
+        subcase: Subcase number (default 1)
+        element_type: Element type ('ctetra', 'chexa', 'cquad4', 'ctria3', or 'auto')
+                     'auto' will detect available element types
+
+    Returns:
+        Dict with max von Mises stress and element info
+    """
+    from pyNastran.op2.op2 import OP2
+    import numpy as np
+
+    model = OP2()
+    model.read_op2(str(op2_file))
+
+    # Auto-detect element type if requested
+    if element_type == 'auto':
+        # Try common element types in order
+        # pyNastran uses "stress.{element}_stress" as attribute names (with dot in name!)
+        possible_types = ['cquad4', 'ctria3', 'ctetra', 'chexa', 'cpenta']
+        element_type = None
+
+        for elem_type in possible_types:
+            stress_attr = f"stress.{elem_type}_stress"
+            try:
+                stress_dict = getattr(model, stress_attr, None)
+                if isinstance(stress_dict, dict) and subcase in stress_dict:
+                    element_type = elem_type
+                    break
+            except AttributeError:
+                continue
+
+        if element_type is None:
+            raise ValueError(f"No stress results found in OP2 for subcase {subcase}")
+
+    # Get stress object for element type
+    # pyNastran stores stress as "stress.{element}_stress" (e.g., "stress.cquad4_stress")
+    stress_attr = f"stress.{element_type}_stress"
+
+    try:
+        stress_dict = getattr(model, stress_attr)
+    except AttributeError:
+        raise ValueError(f"No {element_type} stress results in OP2")
+
+    if not isinstance(stress_dict, dict) or subcase not in stress_dict:
+        raise ValueError(f"Subcase {subcase} not found in {element_type} stress results")
+
+    stress = stress_dict[subcase]
+    itime = 0
+
+    # Extract von Mises
+    # For CQUAD4/CTRIA3 (shells): data shape is [ntimes, nelements, 8]
+    # Columns: [fiber_distance, oxx, oyy, txy, angle, omax, omin, von_mises]
+    # Column 7 (0-indexed) is von Mises
+    #
+    # For CTETRA/CHEXA (solids): Column 9 is von Mises
+
+    if element_type in ['cquad4', 'ctria3']:
+        # Shell elements - von Mises is at column 7
+        von_mises = stress.data[itime, :, 7]
+    else:
+        # Solid elements - von Mises is at column 9
+        von_mises = stress.data[itime, :, 9]
+
+    # Raw stress values from OP2 (in internal Nastran units)
+    max_stress_raw = float(np.max(von_mises))
+    min_stress_raw = float(np.min(von_mises))
+    avg_stress_raw = float(np.mean(von_mises))
+
+    # Convert to MPa
+    # For MN-MM unit system (UNITSYS=MN-MM), Nastran outputs stress with implied decimal
+    # The raw value needs to be divided by 1000 to get MPa
+    # Example: 131507.1875 (raw) = 131.507 MPa
+    max_stress_mpa = max_stress_raw / 1000.0
+    min_stress_mpa = min_stress_raw / 1000.0
+    avg_stress_mpa = avg_stress_raw / 1000.0
+
+    # Get element info
+    if hasattr(stress, 'element_node'):
+        element_ids = stress.element_node[:, 0]  # First column is element ID
+    elif hasattr(stress, 'element'):
+        element_ids = stress.element
+    else:
+        element_ids = np.arange(len(von_mises))
+
+    max_stress_elem = int(element_ids[np.argmax(von_mises)])
+
+    return {
+        'max_von_mises': max_stress_mpa,
+        'min_von_mises': min_stress_mpa,
+        'avg_von_mises': avg_stress_mpa,
+        'max_stress_element': max_stress_elem,
+        'element_type': element_type,
+        'num_elements': len(von_mises),
+        'units': 'MPa'
+    }
+
+
+if __name__ == '__main__':
+    # Example usage
+    import sys
+    if len(sys.argv) > 1:
+        op2_file = Path(sys.argv[1])
+        result = extract_solid_stress(op2_file)
+        print(f"Extraction result: {result}")
+    else:
+        print("Usage: python {sys.argv[0]} <op2_file>")