feat: add neural extraction APIs with NounType taxonomy

Add brain.extract() and brain.extractConcepts() methods that use
NeuralEntityExtractor with embeddings and sophisticated NounType
taxonomy (30+ entity types) for semantic entity and concept extraction.

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

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

src/vfs/types.ts

@@ -66,6 +66,7 @@ export interface VFSMetadata {
     name: string
     confidence: number
   }>
+  conceptNames?: string[]        // Flattened concept names for O(log n) indexed queries
   todos?: VFSTodo[]
   dependencies?: string[]        // For code files - what they import
   exports?: string[]             // For code files - what they export
@@ -343,16 +344,6 @@ export interface VFSConfig {
     autoConcepts?: boolean      // Auto-detect concepts
   }
 
-  // Knowledge Layer - Optional revolutionary enhancement!
-  knowledgeLayer?: {
-    enabled?: boolean           // Enable Knowledge Layer features
-    eventRecording?: boolean    // Track all file operations
-    semanticVersioning?: boolean // Smart versioning based on meaning
-    persistentEntities?: boolean // Track evolving entities
-    concepts?: boolean          // Universal concept system
-    gitBridge?: boolean        // Git import/export support
-  }
-
   // Permissions
   permissions?: {
     defaultFile?: number        // Default file permissions (0o644)