Write pkgs with only ensured assets

[ThanatosGit]

In save_modifications MEDS is creating a modified_pkgs set but it only adds a pkg to the set, if you have modified ressources or have added ressources to it but not if you only have used the ensure_present method. The last method only adds it to _ensured_asset_ids, so it is reasonable to iterate through it and add these pkgs.

This is relevant for MSR as it has a AREA_NAME.pkg but also a AREA_NAME_discardables.pkg. In the first one we ensure all the models, animations etc., while the second contains the scenario BRFLD, lua files and BMSAD.

Let's hope that nothing breaks for Dread (but we are using RomFS export anyways now?)