fix: critical clear() data persistence regression (v5.10.4)

Workshop team reported that brain.clear() doesn't fully delete persistent storage.
After calling clear() and creating a new Brainy instance, all data was restored
from storage. This is a CRITICAL data integrity bug.

Root causes (3 bugs fixed):
1. **FileSystemStorage deleting wrong directory**: Data stored in branches/main/entities/
   but clear() was only deleting old pre-v5.4.0 structure (nouns/, verbs/, metadata/)
2. **COW reinitialization after clear()**: Setting cowEnabled=false on old instance
   doesn't affect new instances. Fixed with persistent marker file.
3. **Metadata index cache not cleared**: find() with type filters returned stale data
   after clear(). Fixed by recreating MetadataIndexManager.

Changes:
- FileSystemStorage: Clear branches/ directory (where data actually lives)
- All storage adapters: Add checkClearMarker()/createClearMarker() methods
- BaseStorage: Check for cow-disabled marker before initializing COW
- Brainy: Recreate metadataIndex after clear() to flush cached data
- Tests: Comprehensive regression suite (8 tests) to prevent recurrence

Fixes Workshop bug report: /media/dpsifr/storage/home/Projects/workshop/BRAINY_V5_10_2_CLEAR_BUG.md

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

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

src/storage/adapters/memoryStorage.ts

@@ -196,6 +196,26 @@ export class MemoryStorage extends BaseStorage {
     }
   }
 
+  /**
+   * Check if COW has been explicitly disabled via clear()
+   * v5.10.4: No-op for MemoryStorage (doesn't persist)
+   * @returns Always false (marker doesn't persist in memory)
+   * @protected
+   */
+  protected async checkClearMarker(): Promise<boolean> {
+    return false // MemoryStorage doesn't persist - marker doesn't survive restart
+  }
+
+  /**
+   * Create marker indicating COW has been explicitly disabled
+   * v5.10.4: No-op for MemoryStorage (doesn't persist)
+   * @protected
+   */
+  protected async createClearMarker(): Promise<void> {
+    // No-op: MemoryStorage doesn't persist, so marker is not needed
+    // clear() in memory already resets all state, no marker survives restart
+  }
+
   /**
    * Save statistics data to storage
    * @param statistics The statistics data to save