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/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 [];