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/intake/__init__.py

@@ -0,0 +1,46 @@
+"""
+Atomizer Intake System
+======================
+
+Provides structured intake processing for optimization studies.
+
+Components:
+- IntakeConfig: Pydantic schema for intake.yaml
+- StudyContext: Complete assembled context for study creation
+- IntakeProcessor: File handling and processing
+- ContextAssembler: Combines all context sources
+
+Usage:
+    from optimization_engine.intake import IntakeProcessor, IntakeConfig
+
+    processor = IntakeProcessor(inbox_folder)
+    context = processor.process()
+"""
+
+from .config import (
+    IntakeConfig,
+    StudyConfig,
+    ObjectiveConfig,
+    ConstraintConfig,
+    DesignVariableConfig,
+    BudgetConfig,
+    AlgorithmConfig,
+    MaterialConfig,
+)
+from .context import StudyContext, IntrospectionData, BaselineResult
+from .processor import IntakeProcessor
+
+__all__ = [
+    "IntakeConfig",
+    "StudyConfig",
+    "ObjectiveConfig",
+    "ConstraintConfig",
+    "DesignVariableConfig",
+    "BudgetConfig",
+    "AlgorithmConfig",
+    "MaterialConfig",
+    "StudyContext",
+    "IntrospectionData",
+    "BaselineResult",
+    "IntakeProcessor",
+]