feat: add entity versioning system with critical bug fixes (v5.3.0)

Entity Versioning (NEW):
- Add complete entity versioning API (brain.versions.*) with 18 methods
- Content-addressable storage with SHA-256 deduplication
- Git-style version control: save, restore, compare, undo, prune
- Auto-versioning augmentation with pattern-based filtering
- Branch-isolated version histories
- Complete integration tests and API documentation

Critical Bug Fixes:
- Fix commit() not updating branch refs (brainy.ts:2385)
  - Root cause: Passed "heads/main" which normalized to "refs/heads/heads/main"
  - Impact: All Git-style versioning features were broken
  - Fix: Pass branch name directly for correct normalization
- Fix VFS entities missing isVFSEntity flag
  - Add isVFSEntity: true to all VFS files/folders for filtering
  - Resolves pollution of semantic search with filesystem entities
  - Updated in writeFile(), mkdir(), and root directory init

Implementation:
- src/versioning/VersionManager.ts - Core versioning engine
- src/versioning/VersionStorage.ts - Content-addressable storage
- src/versioning/VersionIndex.ts - Metadata indexing
- src/versioning/VersionDiff.ts - Version comparison
- src/versioning/VersioningAPI.ts - Public API interface
- src/augmentations/versioningAugmentation.ts - Auto-versioning
- tests/integration/versioning.test.ts - Full integration tests
- tests/unit/versioning/ - Unit test suite

Documentation:
- Complete Entity Versioning API section in docs/api/README.md
- VFS entity filtering guide with examples
- Updated "What's New" section for v5.3.0
- Strategy docs for both critical bugs

Test Results:
- 1168 tests passing
- Build: PASSING (no TypeScript errors)
- Integration tests: ALL PASSING

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

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

src/brainy.ts

@@ -24,6 +24,7 @@ import { NaturalLanguageProcessor } from './neural/naturalLanguageProcessor.js'
 import { NeuralEntityExtractor, ExtractedEntity } from './neural/entityExtractor.js'
 import { TripleIntelligenceSystem } from './triple/TripleIntelligenceSystem.js'
 import { VirtualFileSystem } from './vfs/VirtualFileSystem.js'
+import { VersioningAPI } from './versioning/VersioningAPI.js'
 import { MetadataIndexManager } from './utils/metadataIndex.js'
 import { GraphAdjacencyIndex } from './graph/graphAdjacencyIndex.js'
 import { CommitBuilder } from './storage/cow/CommitObject.js'
@@ -95,6 +96,7 @@ export class Brainy<T = any> implements BrainyInterface<T> {
   private _nlp?: NaturalLanguageProcessor
   private _extractor?: NeuralEntityExtractor
   private _tripleIntelligence?: TripleIntelligenceSystem
+  private _versions?: VersioningAPI
   private _vfs?: VirtualFileSystem
 
   // State
@@ -2380,7 +2382,7 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       const commitHash = await builder.build()
 
       // Update branch ref to point to new commit
-      await refManager.setRef(`heads/${currentBranch}`, commitHash, {
+      await refManager.setRef(currentBranch, commitHash, {
         author: options?.author || 'unknown',
         message: options?.message || 'Snapshot commit'
       })
@@ -2937,6 +2939,38 @@ export class Brainy<T = any> implements BrainyInterface<T> {
     return this._neural
   }
 
+  /**
+   * Versioning API - Entity version control (v5.3.0)
+   *
+   * Provides entity-level versioning with:
+   * - save() - Create version of entity
+   * - restore() - Restore entity to specific version
+   * - list() - List all versions of entity
+   * - compare() - Deep diff between versions
+   * - prune() - Remove old versions (retention policies)
+   *
+   * @example
+   * ```typescript
+   * // Save current state
+   * const version = await brain.versions.save('user-123', { tag: 'v1.0' })
+   *
+   * // List versions
+   * const versions = await brain.versions.list('user-123')
+   *
+   * // Restore to previous version
+   * await brain.versions.restore('user-123', 5)
+   *
+   * // Compare versions
+   * const diff = await brain.versions.compare('user-123', 2, 5)
+   * ```
+   */
+  get versions(): VersioningAPI {
+    if (!this._versions) {
+      this._versions = new VersioningAPI(this as any)
+    }
+    return this._versions
+  }
+
   /**
    * Natural Language Processing API
    */