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/adapters/memoryStorage.ts

@@ -160,6 +160,7 @@ export class MemoryStorage extends BaseStorage {
   /**
    * Clear all data from storage
    * v5.4.0: Clears objectStore (type-first paths)
+   * v7.3.1: Also clears writeCache to prevent stale data after clear
    */
   public async clear(): Promise<void> {
     this.objectStore.clear()
@@ -172,6 +173,11 @@ export class MemoryStorage extends BaseStorage {
     // Clear the statistics cache
     this.statisticsCache = null
     this.statisticsModified = false
+
+    // v7.3.1: Clear write-through cache (inherited from BaseStorage)
+    // Without this, readWithInheritance() would return stale cached data
+    // after clear(), causing "ghost" entities to appear
+    this.clearWriteCache()
   }
 
   /**