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/augmentations/defaultAugmentations.ts

@@ -14,6 +14,7 @@ import { CacheAugmentation } from './cacheAugmentation.js'
 import { MetricsAugmentation } from './metricsAugmentation.js'
 import { MonitoringAugmentation } from './monitoringAugmentation.js'
 import { UniversalDisplayAugmentation } from './universalDisplayAugmentation.js'
+import { KnowledgeAugmentation } from './KnowledgeAugmentation.js'
 
 /**
  * Create default augmentations for zero-config operation
@@ -28,6 +29,7 @@ export function createDefaultAugmentations(
     metrics?: boolean | Record<string, any>
     monitoring?: boolean | Record<string, any>
     display?: boolean | Record<string, any>
+    knowledge?: boolean | Record<string, any>
   } = {}
 ): BaseAugmentation[] {
   const augmentations: BaseAugmentation[] = []
@@ -62,6 +64,11 @@ export function createDefaultAugmentations(
     augmentations.push(new MonitoringAugmentation(monitoringConfig))
   }
 
+  // Knowledge Layer augmentation for VFS intelligence
+  if (config.knowledge !== false) {
+    augmentations.push(new KnowledgeAugmentation() as any)
+  }
+
   return augmentations
 }