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/brainy/add.test.ts

@@ -459,29 +459,8 @@ describe('Brainy.add()', () => {
       )
     })
     
-    it.skip('should handle batch adds efficiently', async () => {
-      // NOTE: Flaky performance test - depends on system load
-      // Arrange
-      const count = 100
-      const params = Array.from({ length: count }, (_, i) => 
-        createAddParams({
-          data: `Batch entity ${i}`,
-          type: 'thing'
-        })
-      )
-      
-      // Act
-      const start = performance.now()
-      const ids = await Promise.all(params.map(p => brain.add(p)))
-      const duration = performance.now() - start
-      
-      // Assert
-      expect(ids).toHaveLength(count)
-      const opsPerSecond = (count / duration) * 1000
-      expect(opsPerSecond).toBeGreaterThan(100) // At least 100 ops/second
-    })
   })
-  
+
   describe('caching behavior', () => {
     it('should retrieve consistent entities', async () => {
       // Arrange (v5.1.0: use valid UUID format)