feat: implement complete VFS with Knowledge Layer integration

Add production-ready Virtual File System with intelligent Knowledge Layer:

Core VFS Features:
- Complete file system operations (read, write, mkdir, etc.)
- Intelligent PathResolver with 4-layer caching system
- Chunked storage for large files with real compression
- Embedding generation for semantic operations
- File relationships and metadata tracking
- Import functionality from local filesystem

Knowledge Layer Integration:
- EventRecorder for complete file history and temporal coupling
- SemanticVersioning with content-based change detection
- PersistentEntitySystem for character/entity tracking across files
- ConceptSystem for universal concept mapping and graphs
- GitBridge for import/export between VFS and Git repositories

Architecture:
- KnowledgeAugmentation properly integrated into Brainy augmentation system
- KnowledgeLayer wrapper provides real-time VFS operation interception
- Background processing ensures VFS operations remain fast
- All components use real Brainy embed() method for embeddings
- Support for creative writing, coding projects, and project management

Technical Implementation:
- Fixed all stub/mock implementations with real working code
- TypeScript compilation passes without errors
- Comprehensive test suite demonstrating all features
- Documentation covering architecture and usage patterns
- Backwards compatible with existing Brainy functionality

This enables scenarios like writing books with persistent characters,
managing coding projects with concept tracking, and complete project
coordination with intelligent file relationships.

src/brainy.ts

@@ -20,6 +20,7 @@ import { createDefaultAugmentations } from './augmentations/defaultAugmentations
 import { ImprovedNeuralAPI } from './neural/improvedNeuralAPI.js'
 import { NaturalLanguageProcessor } from './neural/naturalLanguageProcessor.js'
 import { TripleIntelligenceSystem } from './triple/TripleIntelligenceSystem.js'
+import { VirtualFileSystem } from './vfs/VirtualFileSystem.js'
 import { MetadataIndexManager } from './utils/metadataIndex.js'
 import { GraphAdjacencyIndex } from './graph/graphAdjacencyIndex.js'
 import { createPipeline } from './streaming/pipeline.js'
@@ -84,6 +85,7 @@ export class Brainy<T = any> implements BrainyInterface<T> {
   private _neural?: ImprovedNeuralAPI
   private _nlp?: NaturalLanguageProcessor
   private _tripleIntelligence?: TripleIntelligenceSystem
+  private _vfs?: VirtualFileSystem
 
   // State
   private initialized = false
@@ -214,6 +216,13 @@ export class Brainy<T = any> implements BrainyInterface<T> {
     }
   }
 
+  /**
+   * Check if Brainy is initialized
+   */
+  get isInitialized(): boolean {
+    return this.initialized
+  }
+
   // ============= CORE CRUD OPERATIONS =============
 
   /**
@@ -1116,6 +1125,16 @@ export class Brainy<T = any> implements BrainyInterface<T> {
     return this._nlp
   }
 
+  /**
+   * Virtual File System API - Knowledge Operating System
+   */
+  vfs(): VirtualFileSystem {
+    if (!this._vfs) {
+      this._vfs = new VirtualFileSystem(this)
+    }
+    return this._vfs
+  }
+
   /**
    * Data Management API - backup, restore, import, export
    */