fix: add includeVFS parameter to getRelations() - VFS now visible

CRITICAL BUG FIX - VFS Files Were Completely Invisible

Workshop Team Issue:
- Import created 569 VFS files
- vfs.readdir('/') returned 0 items
- VFS was 100% unusable

Root Cause:
v4.4.0 added includeVFS to brain.find() but FORGOT brain.getRelations().
PathResolver.getChildren() calls getRelations() to find VFS relationships,
but those were being excluded by default - making ALL VFS files invisible!

Fix:
1. Add includeVFS parameter to GetRelationsParams interface
2. Wire includeVFS filtering in brain.getRelations()
   - Excludes VFS relationships by default (metadata.isVFS != true)
   - Include them when includeVFS: true
3. Update VFS to mark all relationships with metadata: { isVFS: true }
   - 7 relate() calls updated in VirtualFileSystem.ts
4. Update PathResolver to use includeVFS: true
   - resolveChild() line 200
   - getChildren() line 229

Impact:
- VFS is now fully functional again
- Consistent with v4.4.0 architecture (VFS separate from knowledge graph)
- All APIs now have includeVFS where needed

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

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

src/vfs/VirtualFileSystem.ts

@@ -422,7 +422,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
         await this.brain.relate({
           from: parentId,
           to: existingId,
-          type: VerbType.Contains
+          type: VerbType.Contains,
+          metadata: { isVFS: true }  // v4.5.1: Mark as VFS relationship
         })
       }
     } else {
@@ -440,7 +441,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
       await this.brain.relate({
         from: parentId,
         to: entity,
-        type: VerbType.Contains
+        type: VerbType.Contains,
+        metadata: { isVFS: true }  // v4.5.1: Mark as VFS relationship
       })
 
       // Update path resolver cache
@@ -762,7 +764,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
         await this.brain.relate({
           from: parentId,
           to: entity,
-          type: VerbType.Contains
+          type: VerbType.Contains,
+          metadata: { isVFS: true }  // v4.5.1: Mark as VFS relationship
         })
       }
 
@@ -1674,7 +1677,12 @@ export class VirtualFileSystem implements IVirtualFileSystem {
       // Add to new parent
       if (newParentPath && newParentPath !== '/') {
         const newParentId = await this.pathResolver.resolve(newParentPath)
-        await this.brain.relate({ from: newParentId, to: entityId, type: VerbType.Contains })
+        await this.brain.relate({
+          from: newParentId,
+          to: entityId,
+          type: VerbType.Contains,
+          metadata: { isVFS: true }  // v4.5.1: Mark as VFS relationship
+        })
       }
     }
 
@@ -1747,7 +1755,12 @@ export class VirtualFileSystem implements IVirtualFileSystem {
     const parentPath = this.getParentPath(destPath)
     if (parentPath && parentPath !== '/') {
       const parentId = await this.pathResolver.resolve(parentPath)
-      await this.brain.relate({ from: parentId, to: newEntity, type: VerbType.Contains })
+      await this.brain.relate({
+        from: parentId,
+        to: newEntity,
+        type: VerbType.Contains,
+        metadata: { isVFS: true }  // v4.5.1: Mark as VFS relationship
+      })
     }
 
     // Update path cache
@@ -1847,7 +1860,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
     await this.brain.relate({
       from: parentId,
       to: entity,
-      type: VerbType.Contains
+      type: VerbType.Contains,
+      metadata: { isVFS: true }  // v4.5.1: Mark as VFS relationship
     })
 
     // Update path resolver cache
@@ -2056,7 +2070,8 @@ export class VirtualFileSystem implements IVirtualFileSystem {
     await this.brain.relate({
       from: fromEntityId,
       to: toEntityId,
-      type: type as any  // Convert string to VerbType
+      type: type as any,  // Convert string to VerbType
+      metadata: { isVFS: true }  // v4.5.1: Mark as VFS relationship
     })
 
     // Invalidate caches for both paths