fix: ensure Contains relationships are maintained when updating files in VFS

- Add Contains relationship verification when updating existing files
- Create missing relationships to prevent orphaned files
- Fix resolvePath to return entity IDs instead of path strings
- Improve error handling in ensureDirectory method
- Add comprehensive tests for Contains relationship integrity

Resolves critical bug where vfs.readdir() returned empty arrays

apps/studio/package.json

@@ -0,0 +1,21 @@
+{
+  "name": "@brainy/studio",
+  "version": "1.0.0",
+  "description": "Brainy Studio - Interactive VFS and Neural Graph Explorer",
+  "type": "module",
+  "scripts": {
+    "start": "npx tsx server.ts",
+    "dev": "npx tsx --watch server.ts"
+  },
+  "dependencies": {
+    "@soulcraft/brainy": "file:../../",
+    "express": "^4.18.2",
+    "cors": "^2.8.5"
+  },
+  "devDependencies": {
+    "@types/express": "^4.17.21",
+    "@types/cors": "^2.8.17",
+    "@types/node": "^20.0.0",
+    "tsx": "^4.19.2"
+  }
+}