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/hnsw/hnswIndex.ts

@@ -681,12 +681,18 @@ export class HNSWIndex {
     queryVector: Vector,
     k: number = 10,
     filter?: (id: string) => Promise<boolean>,
-    options?: { rerank?: { multiplier: number } }
+    options?: { rerank?: { multiplier: number }; candidateIds?: string[] }
   ): Promise<Array<[string, number]>> {
     if (this.nouns.size === 0) {
       return []
     }
 
+    // Metadata-first: convert candidateIds to filter function if no explicit filter
+    if (!filter && options?.candidateIds && options.candidateIds.length > 0) {
+      const candidateSet = new Set(options.candidateIds)
+      filter = async (id: string) => candidateSet.has(id)
+    }
+
     // Check if query vector is defined
     if (!queryVector) {
       throw new Error('Query vector is undefined or null')

src/hnsw/typeAwareHNSWIndex.ts

@@ -257,7 +257,7 @@ export class TypeAwareHNSWIndex {
     k: number = 10,
     type?: NounType | NounType[],
     filter?: (id: string) => Promise<boolean>,
-    options?: { rerank?: { multiplier: number } }
+    options?: { rerank?: { multiplier: number }; candidateIds?: string[] }
   ): Promise<Array<[string, number]>> {
     // Single-type search (fast path)
     if (type && typeof type === 'string') {
@@ -288,7 +288,7 @@ export class TypeAwareHNSWIndex {
     k: number,
     types: NounType[],
     filter?: (id: string) => Promise<boolean>,
-    options?: { rerank?: { multiplier: number } }
+    options?: { rerank?: { multiplier: number }; candidateIds?: string[] }
   ): Promise<Array<[string, number]>> {
     const allResults: Array<[string, number]> = []
 
@@ -323,7 +323,7 @@ export class TypeAwareHNSWIndex {
     queryVector: Vector,
     k: number,
     filter?: (id: string) => Promise<boolean>,
-    options?: { rerank?: { multiplier: number } }
+    options?: { rerank?: { multiplier: number }; candidateIds?: string[] }
   ): Promise<Array<[string, number]>> {
     const allResults: Array<[string, number]> = []