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/intake/InboxSection.tsx

@@ -0,0 +1,147 @@
+/**
+ * InboxSection - Section displaying inbox studies on Home page
+ *
+ * Shows the "Create New Study" card and lists all inbox studies
+ * with their current status and available actions.
+ */
+
+import React, { useState, useEffect, useCallback } from 'react';
+import { Inbox, RefreshCw, ChevronDown, ChevronRight } from 'lucide-react';
+import { intakeApi } from '../../api/intake';
+import { InboxStudy, TopicInfo } from '../../types/intake';
+import { CreateStudyCard } from './CreateStudyCard';
+import { InboxStudyCard } from './InboxStudyCard';
+import { FinalizeModal } from './FinalizeModal';
+
+interface InboxSectionProps {
+  onStudyFinalized?: () => void;
+}
+
+export const InboxSection: React.FC<InboxSectionProps> = ({ onStudyFinalized }) => {
+  const [inboxStudies, setInboxStudies] = useState<InboxStudy[]>([]);
+  const [topics, setTopics] = useState<TopicInfo[]>([]);
+  const [isLoading, setIsLoading] = useState(true);
+  const [isExpanded, setIsExpanded] = useState(true);
+  const [selectedStudyForFinalize, setSelectedStudyForFinalize] = useState<string | null>(null);
+
+  const loadData = useCallback(async () => {
+    setIsLoading(true);
+    try {
+      const [inboxResponse, topicsResponse] = await Promise.all([
+        intakeApi.listInbox(),
+        intakeApi.listTopics(),
+      ]);
+      setInboxStudies(inboxResponse.studies);
+      setTopics(topicsResponse.topics);
+    } catch (err) {
+      console.error('Failed to load inbox data:', err);
+    } finally {
+      setIsLoading(false);
+    }
+  }, []);
+
+  useEffect(() => {
+    loadData();
+  }, [loadData]);
+
+  const handleStudyCreated = (_studyName: string) => {
+    loadData();
+  };
+
+  const handleStudyFinalized = (_finalPath: string) => {
+    setSelectedStudyForFinalize(null);
+    loadData();
+    onStudyFinalized?.();
+  };
+
+  const pendingStudies = inboxStudies.filter(
+    (s) => !['ready', 'running', 'completed'].includes(s.status)
+  );
+
+  return (
+    <div className="space-y-4">
+      {/* Section Header */}
+      <button
+        onClick={() => setIsExpanded(!isExpanded)}
+        className="w-full flex items-center justify-between px-2 py-1 hover:bg-white/5 rounded-lg transition-colors"
+      >
+        <div className="flex items-center gap-3">
+          <div className="w-8 h-8 rounded-lg bg-primary-400/10 flex items-center justify-center">
+            <Inbox className="w-4 h-4 text-primary-400" />
+          </div>
+          <div className="text-left">
+            <h2 className="text-lg font-semibold text-white">Study Inbox</h2>
+            <p className="text-sm text-dark-400">
+              {pendingStudies.length} pending studies
+            </p>
+          </div>
+        </div>
+        <div className="flex items-center gap-2">
+          <button
+            onClick={(e) => {
+              e.stopPropagation();
+              loadData();
+            }}
+            className="p-2 hover:bg-white/5 rounded-lg transition-colors text-dark-400 hover:text-primary-400"
+            title="Refresh"
+          >
+            <RefreshCw className={`w-4 h-4 ${isLoading ? 'animate-spin' : ''}`} />
+          </button>
+          {isExpanded ? (
+            <ChevronDown className="w-5 h-5 text-dark-400" />
+          ) : (
+            <ChevronRight className="w-5 h-5 text-dark-400" />
+          )}
+        </div>
+      </button>
+
+      {/* Content */}
+      {isExpanded && (
+        <div className="space-y-4">
+          {/* Create Study Card */}
+          <CreateStudyCard topics={topics} onStudyCreated={handleStudyCreated} />
+
+          {/* Inbox Studies List */}
+          {inboxStudies.length > 0 && (
+            <div className="space-y-3">
+              <h3 className="text-sm font-medium text-dark-400 px-2">
+                Inbox Studies ({inboxStudies.length})
+              </h3>
+              {inboxStudies.map((study) => (
+                <InboxStudyCard
+                  key={study.study_name}
+                  study={study}
+                  onRefresh={loadData}
+                  onSelect={setSelectedStudyForFinalize}
+                />
+              ))}
+            </div>
+          )}
+
+          {/* Empty State */}
+          {!isLoading && inboxStudies.length === 0 && (
+            <div className="text-center py-8 text-dark-400">
+              <Inbox className="w-12 h-12 mx-auto mb-3 opacity-30" />
+              <p>No studies in inbox</p>
+              <p className="text-sm text-dark-500">
+                Create a new study to get started
+              </p>
+            </div>
+          )}
+        </div>
+      )}
+
+      {/* Finalize Modal */}
+      {selectedStudyForFinalize && (
+        <FinalizeModal
+          studyName={selectedStudyForFinalize}
+          topics={topics}
+          onClose={() => setSelectedStudyForFinalize(null)}
+          onFinalized={handleStudyFinalized}
+        />
+      )}
+    </div>
+  );
+};
+
+export default InboxSection;