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/cli/__init__.py

@@ -0,0 +1,19 @@
+"""
+Atomizer CLI
+============
+
+Command-line interface for Atomizer operations.
+
+Commands:
+- atomizer intake <folder>  - Process an intake folder
+- atomizer validate <study> - Validate a study before running
+- atomizer finalize <study> - Generate final report
+
+Usage:
+    from optimization_engine.cli import main
+    main()
+"""
+
+from .main import main, app
+
+__all__ = ["main", "app"]