fix: add includeVFS to initializeRoot() - prevents duplicate root creation

CRITICAL BUG FIX: VFS.initializeRoot() was calling brain.find() without
includeVFS: true, causing it to exclude VFS entities. This meant it could
never find an existing VFS root, and would create a new one on every init.

This directly caused the Workshop team's issue with ~10 duplicate roots!

All VFS internal methods that call brain.find() or brain.similar() now
correctly use includeVFS: true:
- ✅ initializeRoot() (line 171) - JUST FIXED
- ✅ search() (line 958)
- ✅ findSimilar() (line 1009)
- ✅ searchEntities() (line 2327)

src/vfs/VirtualFileSystem.ts

@@ -167,7 +167,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
         path: '/',           // ✅ Correct field name
         vfsType: 'directory' // ✅ Correct field name
       },
-      limit: 10
+      limit: 10,
+      includeVFS: true  // v4.4.0: CRITICAL - Must find VFS root entity!
     })
 
     if (existing.length > 0) {