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>

optimization_engine/extractors/__init__.py

@@ -65,6 +65,16 @@ from optimization_engine.extractors.extract_zernike_figure import (
     extract_zernike_figure_rms,
 )
 
+# Displacement extraction
+from optimization_engine.extractors.extract_displacement import (
+    extract_displacement,
+)
+
+# Mass extraction from BDF
+from optimization_engine.extractors.extract_mass_from_bdf import (
+    extract_mass_from_bdf,
+)
+
 # Part mass and material extractor (from NX .prt files)
 from optimization_engine.extractors.extract_part_mass_material import (
     extract_part_mass_material,
@@ -145,72 +155,76 @@ from optimization_engine.extractors.spec_extractor_builder import (
 )
 
 __all__ = [
+    # Displacement extraction
+    "extract_displacement",
+    # Mass extraction (from BDF)
+    "extract_mass_from_bdf",
     # Part mass & material (from .prt)
-    'extract_part_mass_material',
-    'extract_part_mass',
-    'extract_part_material',
-    'PartMassExtractor',
+    "extract_part_mass_material",
+    "extract_part_mass",
+    "extract_part_material",
+    "PartMassExtractor",
     # Stress extractors
-    'extract_solid_stress',
-    'extract_principal_stress',
-    'extract_max_principal_stress',
-    'extract_min_principal_stress',
+    "extract_solid_stress",
+    "extract_principal_stress",
+    "extract_max_principal_stress",
+    "extract_min_principal_stress",
     # Strain energy
-    'extract_strain_energy',
-    'extract_total_strain_energy',
-    'extract_strain_energy_density',
+    "extract_strain_energy",
+    "extract_total_strain_energy",
+    "extract_strain_energy_density",
     # SPC forces / reactions
-    'extract_spc_forces',
-    'extract_total_reaction_force',
-    'extract_reaction_component',
-    'check_force_equilibrium',
+    "extract_spc_forces",
+    "extract_total_reaction_force",
+    "extract_reaction_component",
+    "check_force_equilibrium",
     # Zernike (telescope mirrors) - Standard Z-only method
-    'ZernikeExtractor',
-    'extract_zernike_from_op2',
-    'extract_zernike_filtered_rms',
-    'extract_zernike_relative_rms',
+    "ZernikeExtractor",
+    "extract_zernike_from_op2",
+    "extract_zernike_filtered_rms",
+    "extract_zernike_relative_rms",
     # Zernike OPD (RECOMMENDED - uses actual geometry, no shape assumption)
     # Supports annular apertures via inner_radius parameter
-    'ZernikeOPDExtractor',
-    'extract_zernike_opd',
-    'extract_zernike_opd_filtered_rms',
-    'compute_zernike_coefficients_annular',
+    "ZernikeOPDExtractor",
+    "extract_zernike_opd",
+    "extract_zernike_opd_filtered_rms",
+    "compute_zernike_coefficients_annular",
     # Zernike Analytic (parabola-based with lateral displacement correction)
-    'ZernikeAnalyticExtractor',
-    'extract_zernike_analytic',
-    'extract_zernike_analytic_filtered_rms',
-    'compare_zernike_methods',
+    "ZernikeAnalyticExtractor",
+    "extract_zernike_analytic",
+    "extract_zernike_analytic_filtered_rms",
+    "compare_zernike_methods",
     # Backwards compatibility (deprecated)
-    'ZernikeFigureExtractor',
-    'extract_zernike_figure',
-    'extract_zernike_figure_rms',
+    "ZernikeFigureExtractor",
+    "extract_zernike_figure",
+    "extract_zernike_figure_rms",
     # Temperature (Phase 3 - thermal)
-    'extract_temperature',
-    'extract_temperature_gradient',
-    'extract_heat_flux',
-    'get_max_temperature',
+    "extract_temperature",
+    "extract_temperature_gradient",
+    "extract_heat_flux",
+    "get_max_temperature",
     # Modal mass (Phase 3 - dynamics)
-    'extract_modal_mass',
-    'extract_frequencies',
-    'get_first_frequency',
-    'get_modal_mass_ratio',
+    "extract_modal_mass",
+    "extract_frequencies",
+    "get_first_frequency",
+    "get_modal_mass_ratio",
     # Part introspection (Phase 4)
-    'introspect_part',
-    'get_expressions_dict',
-    'get_expression_value',
-    'print_introspection_summary',
+    "introspect_part",
+    "get_expressions_dict",
+    "get_expression_value",
+    "print_introspection_summary",
     # Custom extractor loader (Phase 5)
-    'CustomExtractor',
-    'CustomExtractorLoader',
-    'CustomExtractorContext',
-    'ExtractorSecurityError',
-    'ExtractorValidationError',
-    'load_custom_extractors',
-    'execute_custom_extractor',
-    'validate_custom_extractor',
+    "CustomExtractor",
+    "CustomExtractorLoader",
+    "CustomExtractorContext",
+    "ExtractorSecurityError",
+    "ExtractorValidationError",
+    "load_custom_extractors",
+    "execute_custom_extractor",
+    "validate_custom_extractor",
     # Spec extractor builder
-    'SpecExtractorBuilder',
-    'build_extractors_from_spec',
-    'get_extractor_outputs',
-    'list_available_builtin_extractors',
+    "SpecExtractorBuilder",
+    "build_extractors_from_spec",
+    "get_extractor_outputs",
+    "list_available_builtin_extractors",
 ]