fix(architecture): singleton GraphAdjacencyIndex via storage.getGraphIndex() (v6.3.0)

BREAKING: This is a critical architectural fix for the VFS tree corruption bug
reported by Soulcraft Workshop team. The fix addresses the root cause: dual
ownership of GraphAdjacencyIndex causing verbIdSet to be out of sync.

## Root Cause Analysis

The bug was caused by TWO separate GraphAdjacencyIndex instances:
1. Storage.graphIndex (created in BaseStorage.init())
2. Brainy.graphIndex (created in Brainy.init())

When verbs were saved, both instances were updated. But if Storage's graphIndex
was recreated (via ensureInitialized()), the new instance had an empty verbIdSet.
Queries filtered through this empty verbIdSet returned nothing - making data
appear lost even though it existed in the LSM-trees.

## Fix Summary

1. **GraphAdjacencyIndex Singleton Pattern**
   - Removed direct creation from BaseStorage.init()
   - Brainy now uses `storage.getGraphIndex()` instead of creating its own
   - getGraphIndex() has proper singleton pattern with concurrent access protection
   - Added `invalidateGraphIndex()` for branch switches

2. **Auto-rebuild verbIdSet Defense**
   - Added check in ensureInitialized(): if LSM-trees have data but verbIdSet
     is empty, automatically populate verbIdSet from storage
   - This is a safety net for edge cases

3. **Removed Double-Add Bug**
   - Removed graphIndex.addVerb() from saveVerb_internal()
   - Graph index updates now happen ONLY via AddToGraphIndexOperation in
     Brainy.relate() transaction system
   - This prevents duplicate counting in relationshipCountsByType

4. **PathResolver Cache Invalidation**
   - Added invalidateAllCaches() method to PathResolver and SemanticPathResolver
   - checkout() now clears VFS caches before recreating VFS for new branch

## Files Changed

- src/storage/baseStorage.ts: Removed graphIndex creation from init(), added
  invalidateGraphIndex(), removed addVerb from saveVerb_internal()
- src/brainy.ts: Use storage.getGraphIndex() in init/fork/checkout
- src/graph/graphAdjacencyIndex.ts: Auto-rebuild verbIdSet in ensureInitialized()
- src/vfs/PathResolver.ts: Added invalidateAllCaches()
- src/vfs/semantic/SemanticPathResolver.ts: Added invalidateAllCaches()

## Testing

All VFS tests pass (7/7), including:
- mkdir() should not corrupt VFS index
- Delete and recreate folder cycles
- Contains relationship queries

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/brainy.ts

@@ -231,8 +231,11 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       this.metadataIndex = new MetadataIndexManager(this.storage)
       await this.metadataIndex.init()
 
-      // Initialize core graph index
-      this.graphIndex = new GraphAdjacencyIndex(this.storage)
+      // v6.3.0: Get GraphAdjacencyIndex from storage (SINGLETON pattern)
+      // Storage owns the single instance, Brainy accesses it via getGraphIndex()
+      // This fixes the dual-ownership bug where Brainy and Storage had separate instances
+      // causing verbIdSet to be out of sync and VFS tree queries to fail
+      this.graphIndex = await (this.storage as any).getGraphIndex()
 
       // Rebuild indexes if needed for existing data
       await this.rebuildIndexesIfNeeded()
@@ -2636,8 +2639,14 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       clone.metadataIndex = new MetadataIndexManager(clone.storage)
       await clone.metadataIndex.init()
 
-      clone.graphIndex = new GraphAdjacencyIndex(clone.storage)
-      await clone.graphIndex.rebuild()
+      // v6.3.0: GraphAdjacencyIndex SINGLETON pattern for fork()
+      // Object.create() causes prototype inheritance, so clone.storage.graphIndex
+      // would point to parent's graphIndex. We must break this inheritance and
+      // create a fresh instance for the clone's branch.
+      ;(clone.storage as any).graphIndex = undefined
+      ;(clone.storage as any).graphIndexPromise = undefined
+      clone.graphIndex = await (clone.storage as any).getGraphIndex()
+      // getGraphIndex() will rebuild automatically if data exists (via _initializeGraphIndex)
 
       // Setup augmentations
       clone.augmentationRegistry = this.setupAugmentations()
@@ -2742,7 +2751,12 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       this.index = this.setupIndex()
       this.metadataIndex = new (MetadataIndexManager as any)(this.storage)
       await this.metadataIndex.init()
-      this.graphIndex = new GraphAdjacencyIndex(this.storage)
+
+      // v6.3.0: GraphAdjacencyIndex SINGLETON pattern for checkout()
+      // Invalidate the old graphIndex (it has data from the old branch)
+      // and get a fresh instance for the new branch
+      ;(this.storage as any).invalidateGraphIndex()
+      this.graphIndex = await (this.storage as any).getGraphIndex()
 
       // v5.7.7: Reset lazy loading state when switching branches
       // Indexes contain data from previous branch, must rebuild for new branch
@@ -2751,8 +2765,14 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       // Rebuild indexes from new branch data (force=true to override disableAutoRebuild)
       await this.rebuildIndexesIfNeeded(true)
 
-      // Re-initialize VFS for new branch
+      // v6.3.0: Clear VFS caches before recreating VFS for new branch
+      // UnifiedCache is global, so old branch's VFS path cache entries would persist
       if (this._vfs) {
+        // Clear old PathResolver's caches including UnifiedCache entries
+        if ((this._vfs as any).pathResolver?.invalidateAllCaches) {
+          (this._vfs as any).pathResolver.invalidateAllCaches()
+        }
+        // Recreate VFS for new branch
         this._vfs = new VirtualFileSystem(this)
         await this._vfs.init()
       }