fix: resolve 10 test failures across clustering, metadata, and deletion

Fixed critical bugs affecting test suite:

**Clustering (2 tests fixed)**
- Fixed entity.type field reference bug in _getItemsByField()
- Changed entity.noun to entity.type (correct Entity interface field)
- Now includes ALL entities in domain clustering with 'unknown' fallback

**Relationship Metadata (5 tests fixed)**
- Fixed metadata retrieval in memoryStorage.ts getVerbs()
- Changed metadata.data to metadata.metadata for user's custom metadata
- User metadata now correctly returned in GraphVerb.metadata field

**Delete Relationship Cleanup (2 tests fixed)**
- Added deleteVerbMetadata() method to BaseStorage
- Fixed deleteVerb_internal() in memoryStorage to delete verb metadata
- Relationships now properly cleaned up when entities are deleted

**Validation (1 test fixed)**
- Removed overly restrictive self-referential relationship check
- Self-relationships now allowed (valid in graph systems)

Test results: 27 failures → 17 failures (37% improvement)
All 467 tests now enabled (0 skipped)

src/storage/adapters/memoryStorage.ts

@@ -386,7 +386,7 @@ export class MemoryStorage extends BaseStorage {
     // Iterate through all verbs to find matches
     for (const [verbId, hnswVerb] of this.verbs.entries()) {
       // Get the metadata for this verb to do filtering
-      const metadata = this.verbMetadata.get(verbId)
+      const metadata = await this.getVerbMetadata(verbId)
       
       // Filter by verb type if specified
       if (verbTypes && metadata && !verbTypes.includes(metadata.type || metadata.verb || '')) {
@@ -437,7 +437,7 @@ export class MemoryStorage extends BaseStorage {
     const items: GraphVerb[] = []
     for (const id of paginatedIds) {
       const hnswVerb = this.verbs.get(id)
-      const metadata = this.verbMetadata.get(id)
+      const metadata = await this.getVerbMetadata(id)
       
       if (!hnswVerb) continue
       
@@ -468,7 +468,7 @@ export class MemoryStorage extends BaseStorage {
         updatedAt: metadata.updatedAt,
         createdBy: metadata.createdBy,
         data: metadata.data,
-        metadata: metadata.data // Alias for backward compatibility
+        metadata: metadata.metadata || metadata.data // Use metadata.metadata (user's custom metadata)
       }
       
       items.push(graphVerb)
@@ -525,9 +525,19 @@ export class MemoryStorage extends BaseStorage {
    * Delete a verb from storage
    */
   protected async deleteVerb_internal(id: string): Promise<void> {
-    // Count tracking will be handled when verb metadata is deleted
-    // since HNSWVerb doesn't contain type information
+    // Delete the HNSWVerb from the verbs map
     this.verbs.delete(id)
+
+    // CRITICAL: Also delete verb metadata - this is what getVerbs() uses to find verbs
+    // Without this, getVerbsBySource() will still find "deleted" verbs via their metadata
+    const metadata = await this.getVerbMetadata(id)
+    if (metadata) {
+      const verbType = metadata.verb || metadata.type || 'default'
+      this.decrementVerbCount(verbType)
+
+      // Delete the metadata using the base storage method
+      await this.deleteVerbMetadata(id)
+    }
   }
 
   /**

src/storage/baseStorage.ts

@@ -920,6 +920,16 @@ export abstract class BaseStorage extends BaseStorageAdapter {
     return this.readObjectFromPath(keyInfo.fullPath)
   }
 
+  /**
+   * Delete verb metadata from storage
+   * Uses routing logic to handle both UUIDs (sharded) and system keys (unsharded)
+   */
+  public async deleteVerbMetadata(id: string): Promise<void> {
+    await this.ensureInitialized()
+    const keyInfo = this.analyzeKey(id, 'verb-metadata')
+    return this.deleteObjectFromPath(keyInfo.fullPath)
+  }
+
   /**
    * Save a noun to storage
    * This method should be implemented by each specific adapter