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

src/shared/write-file-atomically.ts

@@ -0,0 +1,13 @@
+import { closeSync, fsyncSync, openSync, renameSync, writeFileSync } from "node:fs"
+
+export function writeFileAtomically(filePath: string, content: string): void {
+  const tempPath = `${filePath}.tmp`
+  writeFileSync(tempPath, content, "utf-8")
+  const tempFileDescriptor = openSync(tempPath, "r")
+  try {
+    fsyncSync(tempFileDescriptor)
+  } finally {
+    closeSync(tempFileDescriptor)
+  }
+  renameSync(tempPath, filePath)
+}