# Root Node Detection Fix

## Problem
The visualization graph incorrectly displayed 380 "root nodes" including 375 functions/classes that should have been nested under their parent files.

## Root Cause
The code used a depth-based fallback that incorrectly included all depth=1 nodes when fewer than 50 root nodes were found. This fallback logic was fundamentally flawed because:
- Functions and classes have depth=1 (they're children of files)
- The fallback treated them as root nodes
- This violated the hierarchical structure of the graph

## Solution
Replaced the depth-based fallback with **link-based detection**:

```javascript
// CORRECT: Find root nodes by checking graph structure
// Root nodes are nodes with no incoming links (no parent)
const targetIds = new Set(allLinks.map(link => link.target));
rootNodes = allNodes.filter(node => !targetIds.has(node.id));
```

### Why This Works
- **Root nodes = nodes with no incoming links**
- In a directed graph, any node that is not a target of any link is a root
- This correctly identifies:
  - ✅ Top-level directories (no parent directory)
  - ✅ Root-level files (not in any directory)
  - ❌ Functions/classes (they have links from their parent files)

## Results

### Before Fix
- **Total Root Nodes**: 380
  - 5 directories ✓
  - 0 files ✗ (should be 4)
  - 375 functions/classes ✗ (should be 0)

### After Fix
- **Total Root Nodes**: 9
  - 5 directories: docs, examples, scripts, src, tests ✓
  - 4 files: CLAUDE.md, PERFORMANCE_OPTIMIZATION_SUMMARY.md, README.md, chunk-graph.json ✓
  - 0 functions ✓
  - 0 classes ✓

## Verification
Run the test script to verify:
```bash
python3 test_root_detection_direct.py
```

Expected output:
```
✓ ALL TESTS PASSED

The link-based root detection correctly identifies:
  - 5 top-level directories
  - 4 root-level files
  - 0 functions (they have parent files)
  - 0 classes (they have parent files)
```

## File Changed
- **Location**: `/Users/masa/Projects/mcp-vector-search/src/mcp_vector_search/visualization/index.html`
- **Lines**: 391-422
- **Change Type**: Logic replacement (depth-based → link-based)

## Impact
- ✅ Graph now shows correct hierarchical structure
- ✅ Users can properly explore the codebase directory by directory
- ✅ No confusion from seeing hundreds of functions as "root" items
- ✅ Performance improved (only 9 initial nodes instead of 380)
