Inside the main folder is mod/ModInfo.xml containing the mods Name/description/version. We have been leaving this up to users to do manually. Currently the only way to change the load order is to rename the folder. Inside the mods folder you place your 'modlets'.
In Alpha 17 the game will now look for a folder called 'Mods' in the root game directory. Not really any specific link as such, but I'll detail as best I can.
