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

tests/unit/hnsw/lazy-vectors.test.ts

@@ -88,7 +88,7 @@ describe('Lazy Vector Loading (B2)', () => {
     })
 
     it('should return correct top-k results in lazy mode', async () => {
-      for (let i = 0; i < 30; i++) {
+      for (let i = 0; i < 50; i++) {
         const id = uuidv4()
         const v = randomVector(dim)
         await saveVector(storage, id, v)