generate_medkit: Modify configuration for package lists

Recetly package lists were expanded by options and they now have their
own configuration file. This makes them incompatible with configuration
done by bootstrap script. This updates bootstrap script to allow usage
of package list options and also removes invalid generation of lists to
updater's config.

The configuration is not replaced by any easy way because we are not
using it and generating another configuration is just too big of a
hustle. Instead we should investigate in future some other way to
generate configuration (for example using package) instead of this.