Modded and vanilla characters/universes could be stored in different folders. If the game detects you using a mod, it loads your modded saves, and you can play in "modded" mode or launch in vanilla mode (not loading any mods and using vanilla storage folder) with a button in the main menu. This will make life really convenient for people who use mods but have a friend who plays vanilla, especially if the person uses steam workshop - there is no easy way to enable disabled mods with it. But the folders must be storage and storagevanilla, because if you make it storage and storagemods, path to already existing saves will change and many mods will break. A lot of great mods are no longer updated, and if the path to something changes, it won't be accounted for.