feat: Dashboard improvements and configuration updates

Dashboard:
- Enhanced terminal components (ClaudeTerminal, GlobalClaudeTerminal)
- Improved MarkdownRenderer for better documentation display
- Updated convergence plots (ConvergencePlot, PlotlyConvergencePlot)
- Refined Home, Analysis, Dashboard, Setup, Results pages
- Added StudyContext improvements
- Updated vite.config for better dev experience

Configuration:
- Updated CLAUDE.md with latest instructions
- Enhanced launch_dashboard.py
- Updated config.py settings

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

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

@@ -227,7 +227,7 @@ export default function Analysis() {
   const isMultiObjective = (metadata?.objectives?.length || 0) > 1;
 
   return (
-    <div className="w-full max-w-[2400px] mx-auto px-4">
+    <div className="w-full">
       {/* Header */}
       <header className="mb-6 flex items-center justify-between border-b border-dark-600 pb-4">
         <div>

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

@@ -375,7 +375,7 @@ export default function Dashboard() {
   };
 
   return (
-    <div className="w-full max-w-[2400px] mx-auto px-4">
+    <div className="w-full">
       {/* Alerts */}
       <div className="fixed top-4 right-4 z-50 space-y-2">
         {alerts.map(alert => (
@@ -436,13 +436,21 @@ export default function Dashboard() {
             <StudyReportViewer studyId={selectedStudyId} />
           )}
           <button
-            onClick={() => {
-              // 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');
+            onClick={async () => {
+              if (!selectedStudyId) return;
+              try {
+                // Launch Optuna dashboard via API, then open the returned URL
+                const result = await apiClient.launchOptunaDashboard(selectedStudyId);
+                window.open(result.url || 'http://localhost:8081', '_blank');
+              } catch (err) {
+                // If launch fails (maybe already running), try opening directly
+                console.warn('Failed to launch dashboard:', err);
+                window.open('http://localhost:8081', '_blank');
+              }
             }}
             className="btn-secondary"
-            title="Open Optuna Dashboard (runs on port 8081)"
+            title="Launch Optuna Dashboard for this study"
+            disabled={!selectedStudyId}
           >
             Optuna Dashboard
           </button>

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

@@ -10,11 +10,16 @@ import {
   FileText,
   ChevronDown,
   ChevronUp,
+  ChevronRight,
   Target,
   Activity,
   BarChart3,
   TrendingUp,
-  ArrowRight
+  ArrowRight,
+  Folder,
+  FolderOpen,
+  Maximize2,
+  X
 } from 'lucide-react';
 import { useStudy } from '../context/StudyContext';
 import { Study } from '../types';
@@ -28,8 +33,64 @@ const Home: React.FC = () => {
   const [readmeLoading, setReadmeLoading] = useState(false);
   const [sortField, setSortField] = useState<'name' | 'status' | 'trials' | 'bestValue'>('trials');
   const [sortDir, setSortDir] = useState<'asc' | 'desc'>('desc');
+  const [expandedTopics, setExpandedTopics] = useState<Set<string>>(new Set());
+  const [isFullscreen, setIsFullscreen] = useState(false);
   const navigate = useNavigate();
 
+  // Group studies by topic, sorted by most recent first
+  const studiesByTopic = useMemo(() => {
+    const grouped: Record<string, Study[]> = {};
+    studies.forEach(study => {
+      const topic = study.topic || 'Other';
+      if (!grouped[topic]) grouped[topic] = [];
+      grouped[topic].push(study);
+    });
+
+    // Sort studies within each topic by last_modified (most recent first)
+    Object.keys(grouped).forEach(topic => {
+      grouped[topic].sort((a, b) => {
+        const aTime = a.last_modified ? new Date(a.last_modified).getTime() : 0;
+        const bTime = b.last_modified ? new Date(b.last_modified).getTime() : 0;
+        return bTime - aTime; // Descending (most recent first)
+      });
+    });
+
+    // Get most recent study time for each topic (for topic sorting)
+    const topicMostRecent: Record<string, number> = {};
+    Object.keys(grouped).forEach(topic => {
+      const mostRecent = grouped[topic][0]?.last_modified;
+      topicMostRecent[topic] = mostRecent ? new Date(mostRecent).getTime() : 0;
+    });
+
+    // Sort topics by most recent study (most recent first), 'Other' always last
+    const sortedTopics = Object.keys(grouped).sort((a, b) => {
+      if (a === 'Other') return 1;
+      if (b === 'Other') return -1;
+      return topicMostRecent[b] - topicMostRecent[a]; // Descending (most recent first)
+    });
+
+    const result: Record<string, Study[]> = {};
+    sortedTopics.forEach(topic => {
+      result[topic] = grouped[topic];
+    });
+    return result;
+  }, [studies]);
+
+  // Topics start collapsed by default - no initialization needed
+  // Users can expand topics by clicking on them
+
+  const toggleTopic = (topic: string) => {
+    setExpandedTopics(prev => {
+      const next = new Set(prev);
+      if (next.has(topic)) {
+        next.delete(topic);
+      } else {
+        next.add(topic);
+      }
+      return next;
+    });
+  };
+
   // Load README when a study is selected for preview
   useEffect(() => {
     if (selectedPreview) {
@@ -235,113 +296,105 @@ const Home: React.FC = () => {
                 <p className="text-sm mt-1 text-dark-500">Create a new study to get started</p>
               </div>
             ) : (
-              <div className="overflow-x-auto max-h-[500px] overflow-y-auto">
-                <table className="w-full">
-                  <thead className="sticky top-0 bg-dark-750 z-10">
-                    <tr className="border-b border-dark-600">
-                      <th
-                        className="text-left py-3 px-4 text-dark-400 font-medium cursor-pointer hover:text-white transition-colors"
-                        onClick={() => handleSort('name')}
-                      >
-                        <div className="flex items-center gap-1">
-                          Study Name
-                          {sortField === 'name' && (
-                            sortDir === 'asc' ? <ChevronUp className="w-4 h-4" /> : <ChevronDown className="w-4 h-4" />
-                          )}
-                        </div>
-                      </th>
-                      <th
-                        className="text-left py-3 px-4 text-dark-400 font-medium cursor-pointer hover:text-white transition-colors"
-                        onClick={() => handleSort('status')}
-                      >
-                        <div className="flex items-center gap-1">
-                          Status
-                          {sortField === 'status' && (
-                            sortDir === 'asc' ? <ChevronUp className="w-4 h-4" /> : <ChevronDown className="w-4 h-4" />
-                          )}
-                        </div>
-                      </th>
-                      <th
-                        className="text-left py-3 px-4 text-dark-400 font-medium cursor-pointer hover:text-white transition-colors"
-                        onClick={() => handleSort('trials')}
-                      >
-                        <div className="flex items-center gap-1">
-                          Progress
-                          {sortField === 'trials' && (
-                            sortDir === 'asc' ? <ChevronUp className="w-4 h-4" /> : <ChevronDown className="w-4 h-4" />
-                          )}
-                        </div>
-                      </th>
-                      <th
-                        className="text-left py-3 px-4 text-dark-400 font-medium cursor-pointer hover:text-white transition-colors"
-                        onClick={() => handleSort('bestValue')}
-                      >
-                        <div className="flex items-center gap-1">
-                          Best
-                          {sortField === 'bestValue' && (
-                            sortDir === 'asc' ? <ChevronUp className="w-4 h-4" /> : <ChevronDown className="w-4 h-4" />
-                          )}
-                        </div>
-                      </th>
-                    </tr>
-                  </thead>
-                  <tbody>
-                    {sortedStudies.map((study) => {
-                      const completionPercent = study.progress.total > 0
-                        ? Math.round((study.progress.current / study.progress.total) * 100)
-                        : 0;
+              <div className="max-h-[500px] overflow-y-auto">
+                {Object.entries(studiesByTopic).map(([topic, topicStudies]) => {
+                  const isExpanded = expandedTopics.has(topic);
+                  const topicTrials = topicStudies.reduce((sum, s) => sum + s.progress.current, 0);
+                  const runningCount = topicStudies.filter(s => s.status === 'running').length;
 
-                      return (
-                        <tr
-                          key={study.id}
-                          onClick={() => setSelectedPreview(study)}
-                          className={`border-b border-dark-700 hover:bg-dark-750 transition-colors cursor-pointer ${
-                            selectedPreview?.id === study.id ? 'bg-primary-900/20' : ''
-                          }`}
-                        >
-                          <td className="py-3 px-4">
-                            <div className="flex flex-col">
-                              <span className="text-white font-medium truncate max-w-[200px]">
-                                {study.name || study.id}
-                              </span>
-                              {study.name && (
-                                <span className="text-xs text-dark-500 truncate max-w-[200px]">{study.id}</span>
-                              )}
-                            </div>
-                          </td>
-                          <td className="py-3 px-4">
-                            <span className={`inline-flex items-center gap-1.5 px-2 py-1 rounded-full text-xs font-medium ${getStatusColor(study.status)}`}>
-                              {getStatusIcon(study.status)}
-                              {study.status}
+                  return (
+                    <div key={topic} className="border-b border-dark-600 last:border-b-0">
+                      {/* Topic Header */}
+                      <button
+                        onClick={() => toggleTopic(topic)}
+                        className="w-full px-4 py-3 flex items-center justify-between hover:bg-dark-750 transition-colors"
+                      >
+                        <div className="flex items-center gap-3">
+                          {isExpanded ? (
+                            <FolderOpen className="w-5 h-5 text-primary-400" />
+                          ) : (
+                            <Folder className="w-5 h-5 text-dark-400" />
+                          )}
+                          <span className="text-white font-medium">{topic.replace(/_/g, ' ')}</span>
+                          <span className="text-dark-500 text-sm">({topicStudies.length})</span>
+                          {runningCount > 0 && (
+                            <span className="flex items-center gap-1 text-xs text-green-400 bg-green-500/10 px-2 py-0.5 rounded-full">
+                              <Play className="w-3 h-3" />
+                              {runningCount} running
                             </span>
-                          </td>
-                          <td className="py-3 px-4">
-                            <div className="flex items-center gap-2">
-                              <div className="flex-1 h-2 bg-dark-600 rounded-full overflow-hidden max-w-[80px]">
-                                <div
-                                  className={`h-full transition-all ${
-                                    completionPercent >= 100 ? 'bg-green-500' :
-                                    completionPercent >= 50 ? 'bg-primary-500' :
-                                    'bg-yellow-500'
-                                  }`}
-                                  style={{ width: `${Math.min(completionPercent, 100)}%` }}
-                                />
+                          )}
+                        </div>
+                        <div className="flex items-center gap-4">
+                          <span className="text-dark-400 text-sm">{topicTrials.toLocaleString()} trials</span>
+                          {isExpanded ? (
+                            <ChevronDown className="w-4 h-4 text-dark-400" />
+                          ) : (
+                            <ChevronRight className="w-4 h-4 text-dark-400" />
+                          )}
+                        </div>
+                      </button>
+
+                      {/* Topic Studies */}
+                      {isExpanded && (
+                        <div className="bg-dark-850">
+                          {topicStudies.map((study) => {
+                            const completionPercent = study.progress.total > 0
+                              ? Math.round((study.progress.current / study.progress.total) * 100)
+                              : 0;
+
+                            return (
+                              <div
+                                key={study.id}
+                                onClick={() => setSelectedPreview(study)}
+                                className={`px-4 py-3 pl-12 flex items-center gap-4 border-t border-dark-700 hover:bg-dark-700 transition-colors cursor-pointer ${
+                                  selectedPreview?.id === study.id ? 'bg-primary-900/20' : ''
+                                }`}
+                              >
+                                {/* Study Name */}
+                                <div className="flex-1 min-w-0">
+                                  <span className="text-white font-medium truncate block">
+                                    {study.name || study.id}
+                                  </span>
+                                  {study.name && (
+                                    <span className="text-xs text-dark-500 truncate block">{study.id}</span>
+                                  )}
+                                </div>
+
+                                {/* Status */}
+                                <span className={`inline-flex items-center gap-1.5 px-2 py-1 rounded-full text-xs font-medium ${getStatusColor(study.status)}`}>
+                                  {getStatusIcon(study.status)}
+                                  {study.status}
+                                </span>
+
+                                {/* Progress */}
+                                <div className="flex items-center gap-2 w-32">
+                                  <div className="flex-1 h-2 bg-dark-600 rounded-full overflow-hidden">
+                                    <div
+                                      className={`h-full transition-all ${
+                                        completionPercent >= 100 ? 'bg-green-500' :
+                                        completionPercent >= 50 ? 'bg-primary-500' :
+                                        'bg-yellow-500'
+                                      }`}
+                                      style={{ width: `${Math.min(completionPercent, 100)}%` }}
+                                    />
+                                  </div>
+                                  <span className="text-dark-400 text-xs font-mono w-14 text-right">
+                                    {study.progress.current}/{study.progress.total}
+                                  </span>
+                                </div>
+
+                                {/* Best Value */}
+                                <span className={`font-mono text-sm w-20 text-right ${study.best_value !== null ? 'text-primary-400' : 'text-dark-500'}`}>
+                                  {study.best_value !== null ? study.best_value.toExponential(2) : 'N/A'}
+                                </span>
                               </div>
-                              <span className="text-dark-400 text-sm font-mono w-16">
-                                {study.progress.current}/{study.progress.total}
-                              </span>
-                            </div>
-                          </td>
-                          <td className="py-3 px-4">
-                            <span className={`font-mono text-sm ${study.best_value !== null ? 'text-primary-400' : 'text-dark-500'}`}>
-                              {study.best_value !== null ? study.best_value.toExponential(3) : 'N/A'}
-                            </span>
-                          </td>
-                        </tr>
-                      );
-                    })}
-                  </tbody>
-                </table>
+                            );
+                          })}
+                        </div>
+                      )}
+                    </div>
+                  );
+                })}
               </div>
             )}
           </div>
@@ -375,21 +428,30 @@ const Home: React.FC = () => {
                 </div>
 
                 {/* Study Quick Stats */}
-                <div className="px-6 py-3 border-b border-dark-600 flex items-center gap-6 text-sm">
-                  <div className="flex items-center gap-2">
-                    {getStatusIcon(selectedPreview.status)}
-                    <span className="text-dark-300 capitalize">{selectedPreview.status}</span>
-                  </div>
-                  <div className="flex items-center gap-2 text-dark-400">
-                    <Activity className="w-4 h-4" />
-                    <span>{selectedPreview.progress.current} / {selectedPreview.progress.total} trials</span>
-                  </div>
-                  {selectedPreview.best_value !== null && (
-                    <div className="flex items-center gap-2 text-primary-400">
-                      <Target className="w-4 h-4" />
-                      <span>Best: {selectedPreview.best_value.toExponential(4)}</span>
+                <div className="px-6 py-3 border-b border-dark-600 flex items-center justify-between text-sm">
+                  <div className="flex items-center gap-6">
+                    <div className="flex items-center gap-2">
+                      {getStatusIcon(selectedPreview.status)}
+                      <span className="text-dark-300 capitalize">{selectedPreview.status}</span>
                     </div>
-                  )}
+                    <div className="flex items-center gap-2 text-dark-400">
+                      <Activity className="w-4 h-4" />
+                      <span>{selectedPreview.progress.current} / {selectedPreview.progress.total} trials</span>
+                    </div>
+                    {selectedPreview.best_value !== null && (
+                      <div className="flex items-center gap-2 text-primary-400">
+                        <Target className="w-4 h-4" />
+                        <span>Best: {selectedPreview.best_value.toExponential(4)}</span>
+                      </div>
+                    )}
+                  </div>
+                  <button
+                    onClick={() => setIsFullscreen(true)}
+                    className="p-2 hover:bg-dark-700 rounded-lg transition-colors text-dark-400 hover:text-white"
+                    title="View fullscreen"
+                  >
+                    <Maximize2 className="w-4 h-4" />
+                  </button>
                 </div>
 
                 {/* README Content */}
@@ -400,7 +462,7 @@ const Home: React.FC = () => {
                       Loading documentation...
                     </div>
                   ) : (
-                    <MarkdownRenderer content={readme} />
+                    <MarkdownRenderer content={readme} studyId={selectedPreview.id} />
                   )}
                 </div>
               </>
@@ -416,6 +478,59 @@ const Home: React.FC = () => {
           </div>
         </div>
       </main>
+
+      {/* Fullscreen README Modal */}
+      {isFullscreen && selectedPreview && (
+        <div className="fixed inset-0 z-50 bg-dark-900/95 backdrop-blur-sm overflow-hidden">
+          <div className="h-full flex flex-col">
+            {/* Modal Header */}
+            <div className="flex-shrink-0 px-8 py-4 border-b border-dark-700 flex items-center justify-between bg-dark-800">
+              <div className="flex items-center gap-4">
+                <div className="w-10 h-10 bg-dark-700 rounded-lg flex items-center justify-center">
+                  <FileText className="w-5 h-5 text-primary-400" />
+                </div>
+                <div>
+                  <h2 className="text-xl font-semibold text-white">
+                    {selectedPreview.name || selectedPreview.id}
+                  </h2>
+                  <p className="text-dark-400 text-sm">Study Documentation</p>
+                </div>
+              </div>
+              <div className="flex items-center gap-3">
+                <button
+                  onClick={() => handleSelectStudy(selectedPreview)}
+                  className="flex items-center gap-2 px-4 py-2 bg-primary-600 hover:bg-primary-500
+                             text-white rounded-lg transition-all font-medium"
+                >
+                  Open Study
+                  <ArrowRight className="w-4 h-4" />
+                </button>
+                <button
+                  onClick={() => setIsFullscreen(false)}
+                  className="p-2 hover:bg-dark-700 rounded-lg transition-colors text-dark-400 hover:text-white"
+                  title="Close fullscreen"
+                >
+                  <X className="w-5 h-5" />
+                </button>
+              </div>
+            </div>
+
+            {/* Modal Content */}
+            <div className="flex-1 overflow-y-auto p-8">
+              <div className="max-w-4xl mx-auto">
+                {readmeLoading ? (
+                  <div className="flex items-center justify-center py-16 text-dark-400">
+                    <RefreshCw className="w-6 h-6 animate-spin mr-3" />
+                    Loading documentation...
+                  </div>
+                ) : (
+                  <MarkdownRenderer content={readme} studyId={selectedPreview.id} />
+                )}
+              </div>
+            </div>
+          </div>
+        </div>
+      )}
     </div>
   );
 };

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

@@ -295,7 +295,7 @@ export default function Results() {
   const visibleParams = showAllParams ? paramEntries : paramEntries.slice(0, 6);
 
   return (
-    <div className="h-full flex flex-col max-w-[2400px] mx-auto px-4">
+    <div className="h-full flex flex-col w-full">
       {/* Header */}
       <header className="mb-6 flex items-center justify-between border-b border-dark-600 pb-4">
         <div>

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

@@ -249,7 +249,7 @@ export default function Setup() {
   }, 1) || 0;
 
   return (
-    <div className="w-full max-w-[2400px] mx-auto px-4">
+    <div className="w-full">
       {/* Header */}
       <header className="mb-6 flex items-center justify-between border-b border-dark-600 pb-4">
         <div>