fix: VFS where clause field names + isVFS flag

CRITICAL FIX: VFS was using incorrect field names in where clauses
- Metadata index stores flat fields: path, vfsType, name
- VFS queried with: 'metadata.path', 'metadata.vfsType' (wrong!)
- Fixed to use correct field names in where clauses

Changes:
- initializeRoot() now uses correct where clause (no workaround needed)
- Added isVFS flag to all VFS entities (mkdir, writeFile, root)
- Updated VFSMetadata type to include isVFS field
- Removed PathResolver fallback (production code, no fallbacks)

This fixes:
- Duplicate root entities (Workshop team had ~10 roots!)
- VFS queries now work correctly with metadata index
- Clean separation between VFS and knowledge graph entities

Production-ready: No mocks, no fallbacks, no workarounds

src/vfs/types.ts

@@ -33,6 +33,7 @@ export interface VFSMetadata {
   name: string                    // Filename or directory name
   parent?: string                 // Parent directory entity ID
   vfsType: 'file' | 'directory' | 'symlink'
+  isVFS?: boolean                 // v4.3.3: Mark as VFS entity (separates from knowledge graph)
 
   // File attributes
   size: number                    // Size in bytes (0 for directories)