feat: Enhance dashboard with charts, study report viewer, and pruning tracking

- Add ConvergencePlot component with running best, statistics, gradient fill
- Add ParameterImportanceChart with Pearson correlation analysis
- Add StudyReportViewer with KaTeX math rendering and full markdown support
- Update pruning endpoint to query Optuna database directly
- Add /report endpoint for STUDY_REPORT.md files
- Fix chart data transformation for single/multi-objective studies
- Update Protocol 13 documentation with new components
- Update generate-report skill with dashboard integration

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

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

docs/04_USER_GUIDES/DASHBOARD.md

@@ -1,6 +1,6 @@
 # Atomizer Dashboard
 
-**Last Updated**: November 23, 2025
+**Last Updated**: December 3, 2025
 
 ---
 
@@ -83,23 +83,50 @@ Displays algorithm information:
 - **Objectives Count**: Number of optimization objectives
 - **Design Variables Count**: Number of design parameters
 
-### 3. Convergence Monitoring
-- **Convergence Plot**: Best value vs. trial number
-- **Real-time Updates**: WebSocket-driven live updates
-- **Pruned Trials**: Visual indication of pruned trials
+### 3. Convergence Plot (Enhanced)
+**File**: `atomizer-dashboard/frontend/src/components/ConvergencePlot.tsx`
 
-### 4. Parameter Space Exploration
-- **2D Scatter Plot**: Design variable relationships
-- **Color Mapping**: Objective values mapped to color intensity
-- **Interactive Tooltips**: Trial details on hover
+Advanced convergence visualization:
+- **Dual-line plot**: Individual trial values + running best trajectory
+- **Area fill**: Gradient under trial values curve
+- **Statistics panel**: Best value, improvement %, 90% convergence trial
+- **Summary footer**: First value, mean, std dev, total trials
+- **Step-after interpolation**: Running best shown as step function
 
-### 5. Trial History Table
+### 4. Parameter Importance Chart
+**File**: `atomizer-dashboard/frontend/src/components/ParameterImportanceChart.tsx`
+
+Correlation-based parameter analysis:
+- **Pearson correlation**: Calculates correlation between each parameter and objective
+- **Horizontal bar chart**: Parameters ranked by absolute importance
+- **Color coding**: Green (negative correlation - helps minimize), Red (positive - hurts minimize)
+- **Tooltip**: Shows percentage importance and raw correlation coefficient (r)
+- **Minimum 3 trials**: Required for statistical significance
+
+### 5. Study Report Viewer
+**File**: `atomizer-dashboard/frontend/src/components/StudyReportViewer.tsx`
+
+Full-featured markdown report viewer:
+- **Modal overlay**: Full-screen report viewing
+- **Math equations**: KaTeX support for LaTeX math (`$...$` inline, `$$...$$` block)
+- **GitHub-flavored markdown**: Tables, code blocks, task lists
+- **Custom styling**: Dark theme with proper typography
+- **Syntax highlighting**: Code blocks with language detection
+- **Refresh button**: Re-fetch report for live updates
+- **External link**: Open in system editor
+
+### 6. Trial History Table
 - Comprehensive list of all trials
 - Sortable columns
 - Status indicators (COMPLETE, PRUNED, FAIL)
 - Parameter values and objective values
 - User attributes (constraints)
 
+### 7. Pruned Trials Tracking
+- **Real-time count**: Fetched directly from Optuna database
+- **Pruning diagnostics**: Tracks pruned trial params and causes
+- **Database query**: Uses SQLite `state = 'PRUNED'` filter
+
 ---
 
 ## API Endpoints
@@ -286,6 +313,9 @@ atomizer-dashboard/
 │   │   │   ├── ParallelCoordinatesPlot.tsx    # Multi-objective visualization
 │   │   │   ├── ParetoPlot.tsx                  # Pareto front scatter plot
 │   │   │   ├── OptimizerPanel.tsx              # Strategy information
+│   │   │   ├── ConvergencePlot.tsx             # Enhanced convergence chart
+│   │   │   ├── ParameterImportanceChart.tsx    # Correlation-based importance
+│   │   │   ├── StudyReportViewer.tsx           # Markdown report viewer
 │   │   │   ├── common/
 │   │   │   │   └── Card.tsx                    # Reusable card component
 │   │   │   └── dashboard/
@@ -307,6 +337,15 @@ atomizer-dashboard/
             └── optimization.py                  # Optimization endpoints
 ```
 
+## NPM Dependencies
+
+The frontend uses these key packages:
+- `react-markdown` - Markdown rendering
+- `remark-gfm` - GitHub-flavored markdown support
+- `remark-math` - Math equation parsing
+- `rehype-katex` - KaTeX math rendering
+- `recharts` - Interactive charts
+
 ---
 
 ## Data Flow
@@ -368,7 +407,16 @@ if (!objectives || !designVariables) return <EmptyState />;
 
 ---
 
-## Future Enhancements
+## Recent Updates (December 2025)
+
+### Completed
+- [x] **Convergence Plot**: Enhanced with running best, statistics, and gradient fill
+- [x] **Parameter Importance Chart**: Correlation analysis with color-coded bars
+- [x] **Study Report Viewer**: Full markdown rendering with KaTeX math support
+- [x] **Pruned Trials**: Real-time count from Optuna database (not JSON file)
+- [x] **Chart Data Transformation**: Fixed `values` array mapping for single/multi-objective
+
+### Future Enhancements
 
 - [ ] 3D Pareto front visualization for 3+ objectives
 - [ ] Advanced filtering and search in trial history