fix: implement stub methods in Neural API clustering

Previously, clusterByDomain() and clusterByTime() methods contained
stub implementations that always returned empty arrays. This caused
empty results when attempting domain-based or temporal clustering.

Changes:
- Implement _getItemsByField() to query brain storage
- Implement _getItemsByTimeWindow() to filter by time windows
- Fix _groupByDomain() to check root, metadata, and data fields
- Implement _findCrossDomainMembers() for cross-domain analysis
- Implement _findCrossDomainClusters() to merge similar clusters
- Add comprehensive tests for domain and time clustering
- Update documentation structure to include VFS guides

The methods now properly query the brain's storage, filter results,
and return functional clustering data.

docs/README.md

@@ -104,6 +104,11 @@ docs/
 │   ├── noun-verb-taxonomy.md  # Data model
 │   ├── triple-intelligence.md # Query system
 │   └── storage.md             # Storage layer
+├── vfs/                       # Virtual Filesystem
+│   ├── README.md              # VFS overview
+│   ├── SEMANTIC_VFS.md        # Semantic projections
+│   ├── VFS_API_GUIDE.md       # Complete API reference
+│   └── QUICK_START.md         # 5-minute setup
 └── api/                       # API documentation
     ├── README.md              # API overview
     ├── brainy-data.md        # Main class