fix: clear() now properly resets VFS and COW state

Bug: After brain.clear(), VFS operations failed with
"Source entity 00000000-0000-0000-0000-000000000000 not found"

Root causes fixed:
- VFS instance remained in memory pointing to deleted root entity
- FileSystemStorage.clear() set blobStorage=undefined but didn't reinit
- Write-through cache returned stale entity data after clear()

Changes:
- Re-initialize COW (BlobStorage) after storage.clear() in brainy.ts
- Reset and reinitialize VFS following checkout() pattern
- Add clearWriteCache() to BaseStorage, call in Memory/FileSystem adapters
- Add 7 integration tests for VFS clear functionality

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

src/storage/baseStorage.ts

@@ -155,6 +155,16 @@ export abstract class BaseStorage extends BaseStorageAdapter {
   // Memory footprint: Bounded by batch size (typically <1000 items during imports)
   private writeCache = new Map<string, any>()
 
+  /**
+   * v7.3.1: Clear the write-through cache
+   * MUST be called by all storage adapter clear() implementations to ensure
+   * read-after-write consistency cache doesn't return stale data after clear.
+   * @protected - Available to subclasses for clear() implementation
+   */
+  protected clearWriteCache(): void {
+    this.writeCache.clear()
+  }
+
   // COW (Copy-on-Write) support - v5.0.0
   public refManager?: RefManager
   public blobStorage?: BlobStorage