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/components/ClaudeTerminal.tsx

@@ -161,15 +161,12 @@ export const ClaudeTerminal: React.FC<ClaudeTerminalProps> = ({
     setIsConnecting(true);
     setError(null);
 
-    // Always use Atomizer root as working directory so Claude has access to:
-    // - CLAUDE.md (system instructions)
-    // - .claude/skills/ (skill definitions)
+    // Let backend determine the working directory (ATOMIZER_ROOT)
     // Pass study_id as parameter so we can inform Claude about the context
-    const workingDir = 'C:/Users/Antoine/Atomizer';
-    const studyParam = selectedStudy?.id ? `&study_id=${selectedStudy.id}` : '';
+    const studyParam = selectedStudy?.id ? `?study_id=${selectedStudy.id}` : '';
 
     const protocol = window.location.protocol === 'https:' ? 'wss:' : 'ws:';
-    const ws = new WebSocket(`${protocol}//${window.location.host}/api/terminal/claude?working_dir=${workingDir}${studyParam}`);
+    const ws = new WebSocket(`${protocol}//${window.location.host}/api/terminal/claude${studyParam}`);
 
     ws.onopen = () => {
       setIsConnected(true);

atomizer-dashboard/frontend/src/components/ConvergencePlot.tsx

@@ -20,8 +20,13 @@ interface Trial {
   trial_number: number;
   values: number[];
   state?: string;
+  constraint_satisfied?: boolean;
+  user_attrs?: Record<string, any>;
 }
 
+// Penalty threshold - objectives above this are considered failed/penalty trials
+const PENALTY_THRESHOLD = 100000;
+
 interface ConvergencePlotProps {
   trials: Trial[];
   objectiveIndex?: number;
@@ -38,9 +43,22 @@ export function ConvergencePlot({
   const convergenceData = useMemo(() => {
     if (!trials || trials.length === 0) return [];
 
-    // Sort by trial number
+    // Sort by trial number, filtering out failed/penalty trials
     const sortedTrials = [...trials]
-      .filter(t => t.values && t.values.length > objectiveIndex && t.state !== 'FAIL')
+      .filter(t => {
+        // Must have valid values
+        if (!t.values || t.values.length <= objectiveIndex) return false;
+        // Filter out failed state
+        if (t.state === 'FAIL') return false;
+        // Filter out penalty values (e.g., 1000000 = solver failure)
+        const val = t.values[objectiveIndex];
+        if (val >= PENALTY_THRESHOLD) return false;
+        // Filter out constraint violations
+        if (t.constraint_satisfied === false) return false;
+        // Filter out pruned trials
+        if (t.user_attrs?.pruned === true || t.user_attrs?.fail_reason) return false;
+        return true;
+      })
       .sort((a, b) => a.trial_number - b.trial_number);
 
     if (sortedTrials.length === 0) return [];

atomizer-dashboard/frontend/src/components/GlobalClaudeTerminal.tsx

@@ -33,12 +33,14 @@ export const GlobalClaudeTerminal: React.FC = () => {
     );
   }
 
-  // Terminal panel
+  // Terminal panel - responsive sizing
+  // On mobile portrait: full width with small margins
+  // On tablet/desktop: fixed size panel
   return (
     <div className={`fixed z-50 transition-all duration-200 ${
       isExpanded
-        ? 'inset-4'
-        : 'bottom-6 right-6 w-[650px] h-[500px]'
+        ? 'inset-2 sm:inset-4'
+        : 'bottom-2 right-2 left-2 h-[400px] sm:bottom-6 sm:right-6 sm:left-auto sm:w-[650px] sm:h-[500px]'
     }`}>
       <ClaudeTerminal
         isExpanded={isExpanded}

atomizer-dashboard/frontend/src/components/MarkdownRenderer.tsx

@@ -10,13 +10,34 @@ import { oneDark } from 'react-syntax-highlighter/dist/esm/styles/prism';
 interface MarkdownRendererProps {
   content: string;
   className?: string;
+  studyId?: string; // Optional study ID for resolving relative image paths
 }
 
 /**
  * Shared markdown renderer with syntax highlighting, GFM, and LaTeX support.
  * Used by both the Home page (README display) and Results page (reports).
  */
-export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({ content, className = '' }) => {
+export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({ content, className = '', studyId }) => {
+  // Helper to resolve image URLs - converts relative paths to API endpoints
+  const resolveImageSrc = (src: string | undefined): string => {
+    if (!src) return '';
+
+    // If it's already an absolute URL or data URL, return as-is
+    if (src.startsWith('http://') || src.startsWith('https://') || src.startsWith('data:')) {
+      return src;
+    }
+
+    // If we have a studyId, route through the API
+    if (studyId) {
+      // Remove leading ./ or / from the path
+      const cleanPath = src.replace(/^\.?\//, '');
+      return `/api/optimization/studies/${studyId}/image/${cleanPath}`;
+    }
+
+    // Fallback: return original src
+    return src;
+  };
+
   return (
     <article className={`markdown-body max-w-none ${className}`}>
       <ReactMarkdown
@@ -165,12 +186,17 @@ export const MarkdownRenderer: React.FC<MarkdownRendererProps> = ({ content, cla
           hr: () => (
             <hr className="my-8 border-dark-600" />
           ),
-          // Images
+          // Images - resolve relative paths through API
           img: ({ src, alt }) => (
             <img
-              src={src}
-              alt={alt}
+              src={resolveImageSrc(src)}
+              alt={alt || ''}
               className="my-4 rounded-lg max-w-full h-auto border border-dark-600"
+              loading="lazy"
+              onError={(e) => {
+                // Hide broken images
+                (e.target as HTMLImageElement).style.display = 'none';
+              }}
             />
           ),
         }}

atomizer-dashboard/frontend/src/components/layout/MainLayout.tsx

@@ -5,8 +5,8 @@ export const MainLayout = () => {
   return (
     <div className="min-h-screen bg-dark-900 text-dark-50 font-sans">
       <Sidebar />
-      <main className="ml-64 min-h-screen">
-        <div className="max-w-7xl mx-auto p-8">
+      <main className="ml-64 min-h-screen p-6">
+        <div className="max-w-6xl">
           <Outlet />
         </div>
       </main>

atomizer-dashboard/frontend/src/components/plotly/PlotlyConvergencePlot.tsx

@@ -19,8 +19,12 @@ interface Trial {
   params: Record<string, number>;
   user_attrs?: Record<string, any>;
   source?: 'FEA' | 'NN' | 'V10_FEA';
+  constraint_satisfied?: boolean;
 }
 
+// Penalty threshold - objectives above this are considered failed/penalty trials
+const PENALTY_THRESHOLD = 100000;
+
 interface PlotlyConvergencePlotProps {
   trials: Trial[];
   objectiveIndex?: number;
@@ -58,6 +62,15 @@ export function PlotlyConvergencePlot({
       const val = t.values?.[objectiveIndex] ?? t.user_attrs?.[objectiveName] ?? null;
       if (val === null || !isFinite(val)) return;
 
+      // Filter out failed/penalty trials:
+      // 1. Objective above penalty threshold (e.g., 1000000 = solver failure)
+      // 2. constraint_satisfied explicitly false
+      // 3. user_attrs indicates pruned/failed
+      const isPenalty = val >= PENALTY_THRESHOLD;
+      const isFailed = t.constraint_satisfied === false;
+      const isPruned = t.user_attrs?.pruned === true || t.user_attrs?.fail_reason;
+      if (isPenalty || isFailed || isPruned) return;
+
       const source = t.source || t.user_attrs?.source || 'FEA';
       const hoverText = `Trial #${t.trial_number}<br>${objectiveName}: ${val.toFixed(4)}<br>Source: ${source}`;