feat: Major update with validators, skills, dashboard, and docs reorganization

- Add validation framework (config, model, results, study validators)
- Add Claude Code skills (create-study, run-optimization, generate-report,
  troubleshoot, analyze-model)
- Add Atomizer Dashboard (React frontend + FastAPI backend)
- Reorganize docs into structured directories (00-09)
- Add neural surrogate modules and training infrastructure
- Add multi-objective optimization support

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

atomizer-dashboard/frontend/src/pages/Dashboard.tsx

@@ -28,6 +28,7 @@ export default function Dashboard() {
   // Protocol 13: New state for metadata and Pareto front
   const [studyMetadata, setStudyMetadata] = useState<any>(null);
   const [paretoFront, setParetoFront] = useState<any[]>([]);
+  const [allTrialsRaw, setAllTrialsRaw] = useState<any[]>([]); // All trials for parallel coordinates
 
   // Load studies on mount
   useEffect(() => {
@@ -117,13 +118,32 @@ export default function Dashboard() {
       fetch(`/api/optimization/studies/${selectedStudyId}/pareto-front`)
         .then(res => res.json())
         .then(paretoData => {
+          console.log('[Dashboard] Pareto front data:', paretoData);
           if (paretoData.is_multi_objective && paretoData.pareto_front) {
+            console.log('[Dashboard] Setting Pareto front with', paretoData.pareto_front.length, 'trials');
             setParetoFront(paretoData.pareto_front);
           } else {
+            console.log('[Dashboard] No Pareto front or not multi-objective');
             setParetoFront([]);
           }
         })
         .catch(err => console.error('Failed to load Pareto front:', err));
+
+      // Fetch ALL trials (not just Pareto) for parallel coordinates
+      fetch(`/api/optimization/studies/${selectedStudyId}/history`)
+        .then(res => res.json())
+        .then(data => {
+          // Transform to match the format expected by ParallelCoordinatesPlot
+          const trialsData = data.trials.map((t: any) => ({
+            trial_number: t.trial_number,
+            values: t.values || [],
+            params: t.design_variables || {},
+            user_attrs: t.user_attrs || {},
+            constraint_satisfied: t.constraint_satisfied !== false
+          }));
+          setAllTrialsRaw(trialsData);
+        })
+        .catch(err => console.error('Failed to load all trials:', err));
     }
   }, [selectedStudyId]);
 
@@ -275,13 +295,12 @@ export default function Dashboard() {
         <div className="flex gap-2">
           <button
             onClick={() => {
-              if (selectedStudyId) {
-                window.open(`http://localhost:8080?study=${selectedStudyId}`, '_blank');
-              }
+              // Open Optuna dashboard on port 8081
+              // Note: The dashboard needs to be started separately with the correct study database
+              window.open('http://localhost:8081', '_blank');
             }}
             className="btn-secondary"
-            disabled={!selectedStudyId}
-            title="Open Optuna Dashboard (make sure it's running on port 8080)"
+            title="Open Optuna Dashboard (runs on port 8081)"
           >
             Optuna Dashboard
           </button>
@@ -355,17 +374,19 @@ export default function Dashboard() {
               <ParetoPlot
                 paretoData={paretoFront}
                 objectives={studyMetadata.objectives}
+                allTrials={allTrialsRaw}
               />
             </div>
           )}
 
           {/* Parallel Coordinates (full width for multi-objective) */}
-          {paretoFront.length > 0 && studyMetadata && studyMetadata.objectives && studyMetadata.design_variables && (
+          {allTrialsRaw.length > 0 && studyMetadata && studyMetadata.objectives && studyMetadata.design_variables && (
             <div className="mb-6">
               <ParallelCoordinatesPlot
-                paretoData={paretoFront}
+                paretoData={allTrialsRaw}
                 objectives={studyMetadata.objectives}
                 designVariables={studyMetadata.design_variables}
+                paretoFront={paretoFront}
               />
             </div>
           )}