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/vfs/VirtualFileSystem.ts

@@ -209,7 +209,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
             path: '/',
             name: '',
             vfsType: 'directory',
-            isVFS: true,  // v4.3.3: Mark as VFS entity
+            isVFS: true,  // v4.3.3: Mark as VFS entity (internal)
+            isVFSEntity: true,  // v5.3.0: Explicit flag for developer filtering
             size: 0,
             permissions: 0o755,
             owner: 'root',
@@ -231,7 +232,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
         path: '/',
         name: '',
         vfsType: 'directory',
-        isVFS: true,  // v4.3.3: Mark as VFS entity
+        isVFS: true,  // v4.3.3: Mark as VFS entity (internal)
+        isVFSEntity: true,  // v5.3.0: Explicit flag for developer filtering
         size: 0,
         permissions: 0o755,
         owner: 'root',
@@ -357,7 +359,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
       name,
       parent: parentId,
       vfsType: 'file',
-      isVFS: true,  // v4.3.3: Mark as VFS entity
+      isVFS: true,  // v4.3.3: Mark as VFS entity (internal)
+      isVFSEntity: true,  // v5.3.0: Explicit flag for developer filtering
       size: buffer.length,
       mimeType,
       extension: this.getExtension(name),
@@ -713,7 +716,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
         name,
         parent: parentId,
         vfsType: 'directory',
-        isVFS: true,  // v4.3.3: Mark as VFS entity
+        isVFS: true,  // v4.3.3: Mark as VFS entity (internal)
+        isVFSEntity: true,  // v5.3.0: Explicit flag for developer filtering
         size: 0,
         permissions: options?.mode || this.config.permissions?.defaultDirectory || 0o755,
         owner: 'user',