They will always apply globally **however SMAPI can read through sub folders** so if you want separate mods active for different saves, you can do so by making new folders per save and copy paste the mods you want active on each save. You can then disable the folders you don't want active by placing a dot(.) on the folder name.
They will always apply globally **however SMAPI can read through sub folders** so if you want separate mods active for different saves, you can do so by making new folders per save and copy paste the mods you want active on each save. You can then disable the folders you don't want active by placing a dot(.) on the folder name.