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/studio/StudioContextFiles.tsx

@@ -0,0 +1,117 @@
+/**
+ * StudioContextFiles - Context document upload and display
+ */
+
+import React, { useState, useRef } from 'react';
+import { FileText, Upload, Trash2, Loader2 } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+
+interface StudioContextFilesProps {
+  draftId: string;
+  files: string[];
+  onUploadComplete: () => void;
+}
+
+export const StudioContextFiles: React.FC<StudioContextFilesProps> = ({
+  draftId,
+  files,
+  onUploadComplete,
+}) => {
+  const [isUploading, setIsUploading] = useState(false);
+  const [deleting, setDeleting] = useState<string | null>(null);
+  const fileInputRef = useRef<HTMLInputElement>(null);
+  
+  const VALID_EXTENSIONS = ['.md', '.txt', '.pdf', '.json', '.csv', '.docx'];
+  
+  const handleFileSelect = async (e: React.ChangeEvent<HTMLInputElement>) => {
+    const selectedFiles = Array.from(e.target.files || []);
+    if (selectedFiles.length === 0) return;
+    
+    e.target.value = '';
+    setIsUploading(true);
+    
+    try {
+      await intakeApi.uploadContextFiles(draftId, selectedFiles);
+      onUploadComplete();
+    } catch (err) {
+      console.error('Failed to upload context files:', err);
+    } finally {
+      setIsUploading(false);
+    }
+  };
+  
+  const deleteFile = async (filename: string) => {
+    setDeleting(filename);
+    
+    try {
+      await intakeApi.deleteContextFile(draftId, filename);
+      onUploadComplete();
+    } catch (err) {
+      console.error('Failed to delete context file:', err);
+    } finally {
+      setDeleting(null);
+    }
+  };
+  
+  const getFileIcon = (_filename: string) => {
+    return <FileText className="w-3.5 h-3.5 text-amber-400" />;
+  };
+  
+  return (
+    <div className="space-y-2">
+      {/* File List */}
+      {files.length > 0 && (
+        <div className="space-y-1">
+          {files.map((name) => (
+            <div
+              key={name}
+              className="flex items-center gap-2 px-2 py-1.5 rounded bg-dark-700/50 text-sm group"
+            >
+              {getFileIcon(name)}
+              <span className="text-dark-200 truncate flex-1">{name}</span>
+              <button
+                onClick={() => deleteFile(name)}
+                disabled={deleting === name}
+                className="p-1 opacity-0 group-hover:opacity-100 hover:bg-red-500/20 rounded text-red-400 transition-all"
+              >
+                {deleting === name ? (
+                  <Loader2 className="w-3 h-3 animate-spin" />
+                ) : (
+                  <Trash2 className="w-3 h-3" />
+                )}
+              </button>
+            </div>
+          ))}
+        </div>
+      )}
+      
+      {/* Upload Button */}
+      <button
+        onClick={() => fileInputRef.current?.click()}
+        disabled={isUploading}
+        className="w-full flex items-center justify-center gap-2 px-3 py-2 rounded-lg
+                   border border-dashed border-dark-600 text-dark-400 text-sm
+                   hover:border-primary-400/50 hover:text-primary-400 hover:bg-primary-400/5
+                   disabled:opacity-50 transition-colors"
+      >
+        {isUploading ? (
+          <Loader2 className="w-4 h-4 animate-spin" />
+        ) : (
+          <Upload className="w-4 h-4" />
+        )}
+        {isUploading ? 'Uploading...' : 'Add context files'}
+      </button>
+      
+      <input
+        ref={fileInputRef}
+        type="file"
+        multiple
+        accept={VALID_EXTENSIONS.join(',')}
+        onChange={handleFileSelect}
+        className="hidden"
+      />
+    </div>
+  );
+};
+
+export default StudioContextFiles;