I was wandering if maybe to either separate the mod into smaller (independent) chunks that can be enabled separately. For example, suppose I only want to have the cool missions from this mod.
So maybe uploading mini-mods to the workshop or somehow adding a configuration option to the mod?

If this is too much work, then I was wandering if just copying directories/files to a new mod location on my side will suffice? I have no experience in modding so I don't know how much dependence there is between the files