Starting Dart 2.17 (as of current planning), dart pub get won't generate .packages anymore. I noticed a few places in Dart-Code that looks for .packages files, for example to determine if dart pub get needs to be run.
Maybe there are other places where .packages is used in Dart-Code?
See: dart-lang/sdk#48272
Side note: The best was to determine if dart pub get needs to run is probably to check that the modification time of pubspec.yaml < pubspec.lock < .dart_tool/package_config.json.