Currently, all mods and such are just dumped right into the "data" folder. This makes it somewhat of a pain to uninstall unwanted mods, or to deal with file conflicts.
I think a good system (following most mod conventions) would be to have a dedicated mods folder, and each mod would get its own folder in it. That folder acts as the mod's own "data" folder, and would be loaded as such on runtime, where it's loaded into memory with the regular game "data" folder. This is how Source games (most notably Garrysmod) handles addons, which makes them easy to install and uninstall without having to pick through the base data folders to delete their individual files.
So for example, for Luke's Extra UFOs mod, they could go into "OpenXcom/Mods/Luke's Extra UFOs/" and that folder would contain the mod's MAPS, ROUTES, Ruleset, and TERRAIN folders. And it can also contain some kind of metadata file as well at its root.
Another small tweak that could be done is the ability to change the order of mods in the Mods screen, this would help resolve conflicts and allow the user to set which ones take precedence (mods lower down the list would overwrite any conflicts of files/ruleset info in mods/base game higher in the list, etc.)
