fix: VFS readdir() no longer returns duplicate entries

- PathResolver.getChildren() now deduplicates by entity ID (v7.4.1)
  This handles duplicate relationship records that can occur when multiple
  Brainy instances create relationships concurrently for the same storage path.

- brain.clear() now invalidates GraphAdjacencyIndex (v7.4.1)
  Prevents stale in-memory index data after clearing storage, which could
  cause relate()'s duplicate check to fail.

Fixes: Workshop bug where readdir('/') returned same directory 13+ times

src/brainy.ts

@@ -2636,6 +2636,15 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       // Clear storage
       await this.storage.clear()
 
+      // v7.4.1: Invalidate GraphAdjacencyIndex to prevent stale in-memory data
+      // The index has LSMTree data and verbIdSet pointing to deleted entities.
+      // Without this, relate()'s duplicate check uses stale data, potentially
+      // allowing duplicate relationships or missing valid duplicates.
+      if (typeof (this.storage as any).invalidateGraphIndex === 'function') {
+        ;(this.storage as any).invalidateGraphIndex()
+      }
+      this.graphIndex = undefined as any
+
       // Reset index
       if ('clear' in this.index && typeof this.index.clear === 'function') {
         await this.index.clear()

src/vfs/PathResolver.ts

@@ -307,8 +307,20 @@ export class PathResolver {
     const childIds = relations.map(r => r.to)
     const childrenMap = await this.brain.batchGet(childIds)
 
+    // v7.4.1: Deduplicate by entity ID to handle duplicate relationship records
+    // This can occur when multiple Brainy instances create relationships concurrently
+    // for the same storage path (each instance has its own in-memory GraphAdjacencyIndex).
+    // The Set lookup is O(1), adding negligible overhead.
+    const seenEntityIds = new Set<string>()
+
     // Process batched results
     for (const relation of relations) {
+      // Skip if we've already processed this entity
+      if (seenEntityIds.has(relation.to)) {
+        continue
+      }
+      seenEntityIds.add(relation.to)
+
       const entity = childrenMap.get(relation.to)
       if (entity && entity.metadata?.vfsType && entity.metadata?.name) {
         validChildren.push(entity as VFSEntity)