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/06_PROTOCOLS_DETAILED/protocol_13_dashboard.md

@@ -1,7 +1,7 @@
 # Protocol 13: Real-Time Dashboard Tracking
 
-**Status**: ✅ COMPLETED
-**Date**: November 21, 2025
+**Status**: ✅ COMPLETED (Enhanced December 2025)
+**Date**: November 21, 2025 (Last Updated: December 3, 2025)
 **Priority**: P1 (Critical)
 
 ## Overview
@@ -130,7 +130,39 @@ Stiffness    Mass    support_angle    tip_thickness
    |  ╱                  ╲                  |
 ```
 
-#### 4. Dashboard Integration
+#### 4. ConvergencePlot Component (NEW - December 2025)
+**File**: `atomizer-dashboard/frontend/src/components/ConvergencePlot.tsx`
+
+**Features**:
+- Dual-line visualization: trial values + running best
+- Area fill gradient under trial curve
+- Statistics header: Best value, Improvement %, 90% convergence trial
+- Summary footer: First value, Mean, Std Dev, Total trials
+- Step-after interpolation for running best line
+- Reference line at best value
+
+#### 5. ParameterImportanceChart Component (NEW - December 2025)
+**File**: `atomizer-dashboard/frontend/src/components/ParameterImportanceChart.tsx`
+
+**Features**:
+- Pearson correlation between parameters and objectives
+- Horizontal bar chart sorted by absolute importance
+- Color coding: Green (negative correlation), Red (positive correlation)
+- Tooltip with percentage and raw correlation coefficient
+- Requires minimum 3 trials for statistical analysis
+
+#### 6. StudyReportViewer Component (NEW - December 2025)
+**File**: `atomizer-dashboard/frontend/src/components/StudyReportViewer.tsx`
+
+**Features**:
+- Full-screen modal for viewing STUDY_REPORT.md
+- KaTeX math equation rendering (`$...$` inline, `$$...$$` block)
+- GitHub-flavored markdown (tables, code blocks, task lists)
+- Custom dark theme styling for all markdown elements
+- Refresh button for live updates
+- External link to open in system editor
+
+#### 7. Dashboard Integration
 **File**: `atomizer-dashboard/frontend/src/pages/Dashboard.tsx`
 
 **Layout Structure**:
@@ -292,6 +324,28 @@ npm run dev  # Runs on port 3001
 - **Real-time writes**: <5ms per trial (JSON serialization)
 - **Dashboard load time**: <500ms initial render
 
+## December 2025 Enhancements
+
+### Completed
+- [x] **ConvergencePlot**: Enhanced with running best, statistics panel, gradient fill
+- [x] **ParameterImportanceChart**: Pearson correlation analysis with color-coded bars
+- [x] **StudyReportViewer**: Full markdown rendering with KaTeX math equation support
+- [x] **Pruning endpoint**: Now queries Optuna SQLite directly instead of JSON file
+- [x] **Report endpoint**: New `/studies/{id}/report` endpoint for STUDY_REPORT.md
+- [x] **Chart data fix**: Proper `values` array transformation for single/multi-objective
+
+### API Endpoint Additions (December 2025)
+
+4. **GET `/api/optimization/studies/{study_id}/pruning`** (Enhanced)
+   - Now queries Optuna database directly for PRUNED trials
+   - Returns params, timing, and pruning cause for each trial
+   - Fallback to legacy JSON file if database unavailable
+
+5. **GET `/api/optimization/studies/{study_id}/report`** (NEW)
+   - Returns STUDY_REPORT.md content as JSON
+   - Searches in 2_results/, 3_results/, and study root
+   - Returns 404 if no report found
+
 ## Future Enhancements (P3)
 
 - [ ] WebSocket support for instant updates (currently polling)
@@ -300,7 +354,6 @@ npm run dev  # Runs on port 3001
 - [ ] Strategy performance comparison charts
 - [ ] Historical phase duration analysis
 - [ ] Mobile-responsive design
-- [ ] Dark/light theme toggle
 
 ## Troubleshooting