For the life of me I can't seem to get Mod Organizer to work correctly with Morrowind. Now, I know there is no official support for Morrowind, but I followed a helpful topic on the Bethsoft forums to trick Mod Organizer into recognizing Morrowind by using an executable for Fallout New Vegas. The thread is here
My problem is that none of the .ESP files are being recognized by the game, MLOX, or any other utility. I take it this is because Mod Organizer doesn't have access to Morrowind.ini where the load order is managed, yet I know other's have gotten Mod Organizer to work regardless.
Am I missing something?