fix: flush all native providers on shutdown to prevent data loss

Shutdown/close/flush now properly flushes all 4 components in parallel:
metadataIndex, graphIndex, HNSW dirty nodes, and storage counts. Previously
only counts were flushed, causing native provider data loss on restart.

Also:
- Wire roaring, msgpack, entityIdMapper provider consumption from plugins
- Fix allOf filter O(n²) intersection → O(n) Set-based
- Fix ne/exists negation filter to use Set-based exclusion
- Add setMsgpackImplementation() swap in SSTable for native msgpack
- Add setRoaringImplementation() swap for native CRoaring bitmaps
- Add getAllIntIds() to EntityIdMapper for bitmap operations
- Remove TypeAwareHNSWIndex from default index creation path
- Export memory detection utilities from internals
- Clean up 26 permanently-skipped dead tests

src/utils/entityIdMapper.ts

@@ -150,6 +150,15 @@ export class EntityIdMapper {
     return this.uuidToInt.size
   }
 
+  /**
+   * Get all mapped integer IDs without storage reads.
+   * Used for bitmap negation operations (ne, exists:false, missing:true)
+   * to avoid full-table getAllIds() scans.
+   */
+  getAllIntIds(): number[] {
+    return Array.from(this.intToUuid.keys())
+  }
+
   /**
    * Convert array of UUIDs to array of integers
    */