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>

atomizer-dashboard/frontend/src/components/canvas/SpecRenderer.tsx

@@ -777,6 +777,8 @@ function SpecRendererInner({
         onConnect={onConnect}
         onInit={(instance) => {
           reactFlowInstance.current = instance;
+          // Auto-fit view on init with padding
+          setTimeout(() => instance.fitView({ padding: 0.2, duration: 300 }), 100);
         }}
         onDragOver={onDragOver}
         onDrop={onDrop}
@@ -785,6 +787,7 @@ function SpecRendererInner({
         onPaneClick={onPaneClick}
         nodeTypes={nodeTypes}
         fitView
+        fitViewOptions={{ padding: 0.2, includeHiddenNodes: false }}
         deleteKeyCode={null} // We handle delete ourselves
         nodesDraggable={editable}
         nodesConnectable={editable}