fix: Knowledge Layer EntityManager integration

* Add EntityManager base class for standardized entity operations
* Update SemanticVersioning to extend EntityManager
* Update EventRecorder to extend EntityManager
* Update PersistentEntitySystem to extend EntityManager
* Update ConceptSystem to extend EntityManager
* Fix entity ID mismatch patterns across all Knowledge Layer components
* Add proper domain ID to Brainy ID mapping
* Replace direct brain.add/find calls with EntityManager methods
* Ensure all entity interfaces extend ManagedEntity
* Add proper metadata fields for querying (eventType, conceptType, entityType)

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/vfs/VirtualFileSystem.ts

@@ -2057,7 +2057,7 @@ export class VirtualFileSystem implements IVirtualFileSystem {
             case 'mkdir':
               await this.mkdir(op.path, op.options)
               break
-            case 'update':
+            case 'update': {
               // Update only metadata without changing content
               const entityId = await this.pathResolver.resolve(op.path)
               await this.brain.update({
@@ -2065,6 +2065,7 @@ export class VirtualFileSystem implements IVirtualFileSystem {
                 metadata: op.options?.metadata
               })
               break
+            }
           }
           result.successful++
         } catch (error: any) {