fix: flush graph LSM-trees on close to prevent data loss across restarts

GraphAdjacencyIndex.flush() was a no-op — LSM MemTables were never
written to SSTables for datasets under the 100K auto-flush threshold.
This caused readdir, getRelations, and getDescendants to return empty
results after close + reopen.

Three fixes:
- LSMTree.get(): merge MemTable + SSTable results (data spans both
  after flush, old early-return missed SSTable data)
- GraphAdjacencyIndex.flush(): actually flush all 4 LSM-trees
- GraphAdjacencyIndex.close(): close all 4 trees (was only closing 2)

Also: brain.close() and shutdown hooks now call close() on graphIndex,
HNSW index, and metadataIndex to release timers and file handles.

src/brainy.ts

@@ -461,7 +461,7 @@ export class Brainy<T = any> implements BrainyInterface<T> {
         let flushedCount = 0
         for (const instance of Brainy.instances) {
           if (instance.initialized) {
-            // Full flush: counts + metadata index + graph index + HNSW dirty nodes
+            // Flush all buffered data, then close to release resources (timers, handles)
             await Promise.all([
               (async () => {
                 if (instance.storage && typeof (instance.storage as any).flushCounts === 'function') {
@@ -484,6 +484,24 @@ export class Brainy<T = any> implements BrainyInterface<T> {
                 }
               })()
             ])
+            // Close components to stop timers that would prevent clean process exit
+            await Promise.all([
+              (async () => {
+                if (instance.graphIndex && typeof instance.graphIndex.close === 'function') {
+                  await instance.graphIndex.close()
+                }
+              })(),
+              (async () => {
+                if (instance.index && typeof (instance.index as any).close === 'function') {
+                  await (instance.index as any).close()
+                }
+              })(),
+              (async () => {
+                if (instance.metadataIndex && typeof (instance.metadataIndex as any).close === 'function') {
+                  await (instance.metadataIndex as any).close()
+                }
+              })(),
+            ])
             flushedCount++
           }
         }
@@ -6702,7 +6720,7 @@ export class Brainy<T = any> implements BrainyInterface<T> {
    * This ensures deferred persistence mode data is saved
    */
   async close(): Promise<void> {
-    // Flush ALL components before closing to prevent data loss
+    // Phase 1: Flush ALL components in parallel to persist buffered data
     // This is critical when cortex native providers buffer data in Rust memory
     await Promise.all([
       // Flush HNSW dirty nodes (deferred persistence mode)
@@ -6731,7 +6749,27 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       })()
     ])
 
-    // Deactivate plugins (safe — all data flushed above)
+    // Phase 2: Close components to release resources (timers, file handles)
+    // Data is already safe on disk from Phase 1
+    await Promise.all([
+      (async () => {
+        if (this.graphIndex && typeof this.graphIndex.close === 'function') {
+          await this.graphIndex.close()
+        }
+      })(),
+      (async () => {
+        if (this.index && typeof (this.index as any).close === 'function') {
+          await (this.index as any).close()
+        }
+      })(),
+      (async () => {
+        if (this.metadataIndex && typeof (this.metadataIndex as any).close === 'function') {
+          await (this.metadataIndex as any).close()
+        }
+      })(),
+    ])
+
+    // Deactivate plugins (safe — all data flushed and resources released above)
     await this.pluginRegistry.deactivateAll()
 
     // Restore console methods if silent mode was enabled
@@ -6751,8 +6789,6 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       }
     }
 
-    // Storage doesn't have close in current interface
-    // We'll just mark as not initialized
     this.initialized = false
   }
 

src/graph/graphAdjacencyIndex.ts

@@ -800,10 +800,21 @@ export class GraphAdjacencyIndex {
 
     const startTime = Date.now()
 
-    // Flush both LSM-trees
-    // Note: LSMTree.close() will handle flushing MemTable
-    // For now, we don't have an explicit flush method in LSMTree
-    // The MemTable will be flushed automatically when threshold is reached
+    // Flush all 4 LSM-trees in parallel (MemTables → SSTables on disk)
+    await Promise.all([
+      this.lsmTreeSource.flush().then(() => {
+        prodLog.debug(`GraphAdjacencyIndex: Flushed source tree`)
+      }),
+      this.lsmTreeTarget.flush().then(() => {
+        prodLog.debug(`GraphAdjacencyIndex: Flushed target tree`)
+      }),
+      this.lsmTreeVerbsBySource.flush().then(() => {
+        prodLog.debug(`GraphAdjacencyIndex: Flushed verbs-by-source tree`)
+      }),
+      this.lsmTreeVerbsByTarget.flush().then(() => {
+        prodLog.debug(`GraphAdjacencyIndex: Flushed verbs-by-target tree`)
+      }),
+    ])
 
     const elapsed = Date.now() - startTime
 
@@ -819,10 +830,14 @@ export class GraphAdjacencyIndex {
       this.flushTimer = undefined
     }
 
-    // Close LSM-trees (will flush MemTables)
+    // Close all 4 LSM-trees (will flush MemTables to SSTables)
     if (this.initialized) {
-      await this.lsmTreeSource.close()
-      await this.lsmTreeTarget.close()
+      await Promise.all([
+        this.lsmTreeSource.close(),
+        this.lsmTreeTarget.close(),
+        this.lsmTreeVerbsBySource.close(),
+        this.lsmTreeVerbsByTarget.close(),
+      ])
     }
 
     prodLog.info('GraphAdjacencyIndex: Shutdown complete')

src/graph/lsm/LSMTree.ts

@@ -296,18 +296,21 @@ export class LSMTree {
   async get(sourceId: string): Promise<string[] | null> {
     const startTime = performance.now()
 
-    // Check MemTable first (hot data)
+    // Merge results from MemTable AND SSTables
+    // Data can span both after a flush (old data in SSTables, new in MemTable)
+    const allTargets = new Set<string>()
+
+    // Check MemTable (hot data)
     const memResult = this.memTable.get(sourceId)
     if (memResult !== null) {
-      return memResult
+      for (const target of memResult) {
+        allTargets.add(target)
+      }
     }
 
     // Check SSTables from newest to oldest
-    // Newer levels (L0, L1, L2) checked first for better cache locality
     const maxLevel = Math.max(...Array.from(this.sstablesByLevel.keys()), 0)
 
-    const allTargets = new Set<string>()
-
     for (let level = 0; level <= maxLevel; level++) {
       const sstables = this.sstablesByLevel.get(level) || []
 
@@ -608,16 +611,20 @@ export class LSMTree {
   }
 
   /**
-   * Flush MemTable and stop compaction
-   * Called during shutdown
+   * Flush MemTable to SSTables without closing
+   * Called by GraphAdjacencyIndex.flush() and brain.close()
    */
+  async flush(): Promise<void> {
+    if (!this.memTable.isEmpty()) {
+      await this.flushMemTable()
+    }
+  }
+
   async close(): Promise<void> {
     this.stopCompactionTimer()
 
     // Final MemTable flush
-    if (!this.memTable.isEmpty()) {
-      await this.flushMemTable()
-    }
+    await this.flush()
 
     prodLog.info('LSMTree: Closed successfully')
   }

tests/unit/vfs-restart-fix.test.ts

@@ -0,0 +1,133 @@
+/**
+ * Regression test: VFS data persists across restart (close + reopen)
+ *
+ * Verifies the fix for GraphAdjacencyIndex.flush() and LSMTree.get()
+ * which previously caused graph relationships to be lost on restart
+ * because LSM MemTables were never flushed to SSTables on close.
+ */
+import { describe, it, expect } from 'vitest'
+import { Brainy } from '../../src/brainy.js'
+import { VerbType } from '../../src/types/graphTypes.js'
+import { mkdirSync, rmSync } from 'fs'
+
+describe('VFS restart persistence', () => {
+  it('entities and relationships survive close + reopen', async () => {
+    const dir = '/tmp/brainy-restart-fix-' + Date.now()
+    mkdirSync(dir, { recursive: true })
+
+    let entityId: string | undefined
+    const rootId = '00000000-0000-0000-0000-000000000000'
+
+    try {
+      // === SESSION 1: Write data ===
+      let brain = new Brainy({
+        storage: { type: 'filesystem', rootDirectory: dir },
+        disableAutoRebuild: true,
+        plugins: [],
+        silent: true,
+      })
+      await brain.init()
+
+      await brain.vfs.writeFile('/chapter-1.txt', 'Once upon a time...')
+
+      entityId = await brain.vfs.resolvePathToId('/chapter-1.txt')
+      expect(entityId).toBeTruthy()
+
+      // Verify within same session
+      const entity1 = await brain.get(entityId!)
+      expect(entity1).not.toBeNull()
+
+      const entries1 = await brain.vfs.readdir('/')
+      expect(entries1.length).toBeGreaterThan(0)
+
+      await brain.close()
+
+      // === SESSION 2: Read data after restart ===
+      brain = new Brainy({
+        storage: { type: 'filesystem', rootDirectory: dir },
+        disableAutoRebuild: true,
+        plugins: [],
+        silent: true,
+      })
+      await brain.init()
+
+      // Entity should be retrievable
+      const entity2 = await brain.get(entityId!)
+      expect(entity2).not.toBeNull()
+
+      // Root entity should exist
+      const rootEntity = await brain.get(rootId)
+      expect(rootEntity).not.toBeNull()
+
+      // readdir should return the file
+      const entries2 = await brain.vfs.readdir('/')
+      expect(entries2.length).toBeGreaterThan(0)
+      expect(entries2).toContain('chapter-1.txt')
+
+      // getRelations should find the Contains relationship
+      const relations2 = await brain.getRelations({ from: rootId, type: VerbType.Contains })
+      expect(relations2.length).toBeGreaterThan(0)
+
+      await brain.close()
+    } finally {
+      try { rmSync(dir, { recursive: true }) } catch {}
+    }
+  })
+
+  it('multiple files and subdirectories survive restart', async () => {
+    const dir = '/tmp/brainy-restart-multi-' + Date.now()
+    mkdirSync(dir, { recursive: true })
+
+    const rootId = '00000000-0000-0000-0000-000000000000'
+
+    try {
+      // === SESSION 1: Write multiple files ===
+      let brain = new Brainy({
+        storage: { type: 'filesystem', rootDirectory: dir },
+        disableAutoRebuild: true,
+        plugins: [],
+        silent: true,
+      })
+      await brain.init()
+
+      await brain.vfs.writeFile('/readme.txt', 'Project readme')
+      await brain.vfs.writeFile('/docs/guide.txt', 'User guide')
+      await brain.vfs.writeFile('/docs/api.txt', 'API reference')
+
+      const entries1 = await brain.vfs.readdir('/')
+      expect(entries1.length).toBe(2) // readme.txt + docs/
+
+      const docEntries1 = await brain.vfs.readdir('/docs')
+      expect(docEntries1.length).toBe(2) // guide.txt + api.txt
+
+      await brain.close()
+
+      // === SESSION 2: Verify all data persisted ===
+      brain = new Brainy({
+        storage: { type: 'filesystem', rootDirectory: dir },
+        disableAutoRebuild: true,
+        plugins: [],
+        silent: true,
+      })
+      await brain.init()
+
+      // Root children
+      const entries2 = await brain.vfs.readdir('/')
+      expect(entries2.length).toBe(2)
+      expect(entries2.sort()).toEqual(['docs', 'readme.txt'])
+
+      // Subdirectory children
+      const docEntries2 = await brain.vfs.readdir('/docs')
+      expect(docEntries2.length).toBe(2)
+      expect(docEntries2.sort()).toEqual(['api.txt', 'guide.txt'])
+
+      // Root relations
+      const rootRelations = await brain.getRelations({ from: rootId, type: VerbType.Contains })
+      expect(rootRelations.length).toBeGreaterThan(0)
+
+      await brain.close()
+    } finally {
+      try { rmSync(dir, { recursive: true }) } catch {}
+    }
+  })
+})