There are some stacks which are not designed to work with each other and should not both be installed. Some basic validation would be really useful to give feedback to the user when this occurs. E.g.
Because both packages include a phpcs.xml file, only one of the stubs will be installed as stubs are designed to not replace files if they already exist. You should only install one of these stacks depending on your environment (e.g. laravel is a custom php stack)