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/transaction/operations/IndexOperations.ts

@@ -2,8 +2,7 @@
  * Index Operations with Rollback Support
  *
  * Provides transactional operations for all indexes:
- * - TypeAwareHNSWIndex (per-type vector indexes)
- * - HNSWIndex (legacy/fallback vector index)
+ * - HNSWIndex (unified vector index)
  * - MetadataIndexManager (roaring bitmap filtering)
  * - GraphAdjacencyIndex (LSM-tree graph storage)
  *
@@ -11,10 +10,8 @@
  */
 
 import type { HNSWIndex } from '../../hnsw/hnswIndex.js'
-import type { TypeAwareHNSWIndex } from '../../hnsw/typeAwareHNSWIndex.js'
 import type { MetadataIndexManager } from '../../utils/metadataIndex.js'
 import type { GraphAdjacencyIndex } from '../../graph/graphAdjacencyIndex.js'
-import type { NounType } from '../../types/graphTypes.js'
 import type { GraphVerb } from '../../coreTypes.js'
 import type { Operation, RollbackAction } from '../types.js'
 
@@ -67,55 +64,6 @@ export class AddToHNSWOperation implements Operation {
   }
 }
 
-/**
- * Add to TypeAwareHNSW index with rollback support
- *
- * Rollback strategy:
- * - Remove item from type-specific index
- */
-export class AddToTypeAwareHNSWOperation implements Operation {
-  readonly name = 'AddToTypeAwareHNSW'
-
-  constructor(
-    private readonly index: TypeAwareHNSWIndex,
-    private readonly id: string,
-    private readonly vector: number[],
-    private readonly nounType: NounType
-  ) {}
-
-  async execute(): Promise<RollbackAction> {
-    // Check if item already exists
-    const existed = await this.itemExists(this.id, this.nounType)
-
-    // Add to type-specific index
-    await this.index.addItem({ id: this.id, vector: this.vector }, this.nounType)
-
-    // Return rollback action
-    return async () => {
-      if (!existed) {
-        // Remove newly added item from type-specific index
-        await this.index.removeItem(this.id, this.nounType)
-      }
-    }
-  }
-
-  /**
-   * Check if item exists in type-specific index
-   */
-  private async itemExists(id: string, type: NounType): Promise<boolean> {
-    try {
-      const index = (this.index as any).getIndexForType?.(type)
-      if (index) {
-        await index.getItem?.(id)
-        return true
-      }
-      return false
-    } catch {
-      return false
-    }
-  }
-}
-
 /**
  * Remove from HNSW index with rollback support
  *
@@ -145,34 +93,6 @@ export class RemoveFromHNSWOperation implements Operation {
   }
 }
 
-/**
- * Remove from TypeAwareHNSW index with rollback support
- *
- * Rollback strategy:
- * - Re-add item to type-specific index with original vector
- */
-export class RemoveFromTypeAwareHNSWOperation implements Operation {
-  readonly name = 'RemoveFromTypeAwareHNSW'
-
-  constructor(
-    private readonly index: TypeAwareHNSWIndex,
-    private readonly id: string,
-    private readonly vector: number[], // Required for rollback
-    private readonly nounType: NounType
-  ) {}
-
-  async execute(): Promise<RollbackAction> {
-    // Remove from type-specific index
-    await this.index.removeItem(this.id, this.nounType)
-
-    // Return rollback action
-    return async () => {
-      // Re-add item with original vector to type-specific index
-      await this.index.addItem({ id: this.id, vector: this.vector }, this.nounType)
-    }
-  }
-}
-
 /**
  * Add to metadata index with rollback support
  *

src/transaction/operations/index.ts

@@ -22,9 +22,7 @@ export {
 // Index Operations
 export {
   AddToHNSWOperation,
-  AddToTypeAwareHNSWOperation,
   RemoveFromHNSWOperation,
-  RemoveFromTypeAwareHNSWOperation,
   AddToMetadataIndexOperation,
   RemoveFromMetadataIndexOperation,
   AddToGraphIndexOperation,