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/graph/lsm/SSTable.ts

@@ -14,9 +14,23 @@
  * - Footer: checksum, stats
  */
 
-import { encode, decode } from '@msgpack/msgpack'
+import { encode as defaultEncode, decode as defaultDecode } from '@msgpack/msgpack'
 import { BloomFilter, SerializedBloomFilter } from './BloomFilter.js'
 
+// Swappable msgpack implementation — defaults to @msgpack/msgpack JS,
+// can be replaced with native msgpack (e.g., cortex's Rust-backed encoder)
+let _encode: (data: unknown) => Uint8Array = defaultEncode as (data: unknown) => Uint8Array
+let _decode: (data: Uint8Array) => unknown = defaultDecode as (data: Uint8Array) => unknown
+
+/**
+ * Replace the msgpack encode/decode implementation at runtime.
+ * Called by brainy.ts when a cortex 'msgpack' provider is registered.
+ */
+export function setMsgpackImplementation(impl: { encode: (data: unknown) => Uint8Array, decode: (data: Uint8Array) => unknown }) {
+  _encode = impl.encode
+  _decode = impl.decode
+}
+
 /**
  * Entry in the SSTable
  * Maps a source node to its target nodes
@@ -299,7 +313,7 @@ export class SSTable {
       checksum: this.calculateChecksum(this.entries)
     }
 
-    const serialized = encode(data)
+    const serialized = _encode(data)
 
     // Update size in metadata
     this.metadata.sizeBytes = serialized.length
@@ -331,7 +345,7 @@ export class SSTable {
    * @returns SSTable instance
    */
   static deserialize(data: Uint8Array): SSTable {
-    const decoded = decode(data) as SerializedSSTable
+    const decoded = _decode(data) as SerializedSSTable
 
     // Verify checksum
     const sstable = new SSTable(