To clarify, the official mod support will include three mod categories; "cosmetic", "serveronly", and "requiredbyall" (names are not final).
Cosmetic mods are mods that only you can see. This could be minor UI changes, HUD modifications, anime profile pics, or meme sound bites.
Server-only mods are mods that change the basic rules of the missions, like the amount of gunk seeds in the level, nitra- cost for resupplies, etc,
Requiredbyall mods are mods that will change the character, like giving the engineer more turrets, etc.
Cosmetic mods will have no influence on gameplay as such, and will not be separated. The other two categories can change the gameplay and will prompt you to play on a separate save game, either a clone of your unmodded save or a fresh save. You can always copy your unmodded save to a modded save slot, but not the other way around.
Modded savegames can't see unmodded games, and unmodded savegames can't see modded games. The idea...
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