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/PathResolver.ts

@@ -224,7 +224,7 @@ export class PathResolver {
    * Uses proper graph relationships to traverse the tree
    */
   async getChildren(dirId: string): Promise<VFSEntity[]> {
-    // Use proper graph API to get all Contains relationships from this directory
+    // Production-ready: Use graph relationships (VFS creates these in mkdir/writeFile)
     const relations = await this.brain.getRelations({
       from: dirId,
       type: VerbType.Contains
@@ -233,7 +233,7 @@ export class PathResolver {
     const validChildren: VFSEntity[] = []
     const childNames = new Set<string>()
 
-    // Fetch all child entities
+    // Fetch all child entities via relationships
     for (const relation of relations) {
       const entity = await this.brain.get(relation.to)
       if (entity && entity.metadata?.vfsType && entity.metadata?.name) {