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);