Re: Running a Feed the Beast Minecraft server on Lubuntu.
I am not familiar with Feed the Beast Minecraft. But I know that when I ran a Tekkit server just to get familiar with that, it kept some of its files in one visible directory that I created, and other files (including an older minecraft version) in a hidden directory (beginning with a dot) in my home dir. In the file manager if you hit Ctrl-H you can see hidden folders.
In any case if you are running a minecraft server with mods, it should not be in the same directory as your plain vanilla minecraft server.
i5 650 3.2 GHz, 8 GB, nvidia GTX 1060, 32" 1080p & assorted older computers