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/brainy.ts

@@ -2196,7 +2196,7 @@ export class Brainy<T = any> implements BrainyInterface<T> {
     return this.augmentationRegistry.execute('clear', {}, async () => {
       // Clear storage
       await this.storage.clear()
-      
+
       // Reset index
       if ('clear' in this.index && typeof this.index.clear === 'function') {
         await this.index.clear()
@@ -2204,10 +2204,15 @@ export class Brainy<T = any> implements BrainyInterface<T> {
         // Recreate index if no clear method
         this.index = this.setupIndex()
       }
-      
+
+      // v5.10.4: Recreate metadata index to clear cached data
+      // Bug: Metadata index cache was not being cleared, causing find() with type filters to return stale data
+      this.metadataIndex = new MetadataIndexManager(this.storage)
+      await this.metadataIndex.init()
+
       // Reset dimensions
       this.dimensions = undefined
-      
+
       // Clear any cached sub-APIs
       this._neural = undefined
       this._nlp = undefined