Rename safeOutputFile to atomicOverwriteFile (#1167)

"safe" suggested the data being written survives a crash, it only
guarantees the old file is either kept or fully replaced. The new name
says what it does. No alias, plugin API breaks are allowed in minor
versions and the 2.1 migration guide lists the rename.

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Cooldude2606 <25043174+Cooldude2606@users.noreply.github.com>

packages/controller/controller.ts

@@ -209,7 +209,7 @@ async function handleBootstrapCommand(
 			console.log(content);
 		} else {
 			logger.info(`Writing ${args.output}`);
-			await lib.safeOutputFile(args.output, content, { mode: 0o600 });
+			await lib.atomicOverwriteFile(args.output, content, { mode: 0o600 });
 		}
 	}
 }