The mods are loaded in no particular order and there isn't any way to set the mod order. What I do know is if you subscribe to mods in the workshop they have a numerical tag and are loaded in that order. If you download mods from Nexus you have to move them to your "C:\Users\(username)\AppData\Roaming\Jagged Alliance 3\mods" folder. They will be will then be loaded alphabetically.

I'm sure someone will correct me if I've gotten something wrong.

Originally posted by Notoko:

Does mod order make any difference?

Is there a way to set the mod order?

There is a load order and although the stem mod manager does it for you, you can change it manually, and yes it can affect you game.

You can affect load order by setting dependency. Obvisouly, if you have mod A and mod B and you create mod A being dependent on mod B, then mod B has to be loaded before mod A.

If you load loads of mods and want to use incompatible mods with each other and you want to decide the load order, it is a good idea to go into editor and set the dependency of the inferior mod towards the superior mod and save it with a custom name.