fix(config): use canonical path after legacy migration and make writes atomic

src/shared/index.ts

@@ -28,6 +28,7 @@ export * from "./permission-compat"
 export * from "./external-plugin-detector"
 export * from "./zip-extractor"
 export * from "./binary-downloader"
+export * from "./write-file-atomically"
 export * from "./agent-variant"
 export * from "./session-cursor"
 export * from "./shell-env"