feat: Add Studio UI, intake system, and extractor improvements

Dashboard:
- Add Studio page with drag-drop model upload and Claude chat
- Add intake system for study creation workflow
- Improve session manager and context builder
- Add intake API routes and frontend components

Optimization Engine:
- Add CLI module for command-line operations
- Add intake module for study preprocessing
- Add validation module with gate checks
- Improve Zernike extractor documentation
- Update spec models with better validation
- Enhance solve_simulation robustness

Documentation:
- Add ATOMIZER_STUDIO.md planning doc
- Add ATOMIZER_UX_SYSTEM.md for UX patterns
- Update extractor library docs
- Add study-readme-generator skill

Tools:
- Add test scripts for extraction validation
- Add Zernike recentering test

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

docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md

@@ -110,31 +110,48 @@ frequency = result['frequency']  # Hz
 ```python
 from optimization_engine.extractors.extract_von_mises_stress import extract_solid_stress
 
-# For shell elements (CQUAD4, CTRIA3)
-result = extract_solid_stress(op2_file, subcase=1, element_type='cquad4')
+# RECOMMENDED: Check ALL solid element types (returns max across all)
+result = extract_solid_stress(op2_file, subcase=1)
 
-# For solid elements (CTETRA, CHEXA)
-result = extract_solid_stress(op2_file, subcase=1, element_type='ctetra')
+# Or specify single element type
+result = extract_solid_stress(op2_file, subcase=1, element_type='chexa')
 
 # Returns: {
-#     'max_von_mises': float,    # MPa
-#     'max_stress_element': int
+#     'max_von_mises': float,      # MPa (auto-converted from kPa)
+#     'max_stress_element': int,
+#     'element_type': str,         # e.g., 'CHEXA', 'CTETRA'
+#     'units': 'MPa'
 # }
 
 max_stress = result['max_von_mises']  # MPa
 ```
 
+**IMPORTANT (Updated 2026-01-22):**
+- By default, checks ALL solid types: CTETRA, CHEXA, CPENTA, CPYRAM
+- CHEXA elements often have highest stress (not CTETRA!)
+- Auto-converts from kPa to MPa (NX kg-mm-s unit system outputs kPa)
+- Returns Elemental Nodal stress (peak), not Elemental Centroid (averaged)
+
 ### E4: BDF Mass Extraction
 
-**Module**: `optimization_engine.extractors.bdf_mass_extractor`
+**Module**: `optimization_engine.extractors.extract_mass_from_bdf`
 
 ```python
-from optimization_engine.extractors.bdf_mass_extractor import extract_mass_from_bdf
+from optimization_engine.extractors import extract_mass_from_bdf
 
-mass_kg = extract_mass_from_bdf(str(bdf_file))  # kg
+result = extract_mass_from_bdf(bdf_file)
+# Returns: {
+#     'total_mass': float,    # kg (primary key)
+#     'mass_kg': float,       # kg
+#     'mass_g': float,        # grams
+#     'cg': [x, y, z],        # center of gravity
+#     'num_elements': int
+# }
+
+mass_kg = result['mass_kg']  # kg
 ```
 
-**Note**: Reads mass directly from BDF/DAT file material and element definitions.
+**Note**: Uses `BDFMassExtractor` internally. Reads mass from element geometry and material density in BDF/DAT file. NX kg-mm-s unit system - mass is directly in kg.
 
 ### E5: CAD Expression Mass