http://forums.legionsoverdrive.com/threads/linux-dedicated-server-binaries.3729/#post-73842
Use the search bar next time.
Found that information already, with the search.
After looking over all the post again, this is what I was looking for.
./Legions.linux --log-dir=server1 --mod-list=modList_Server.txt --server-config=server1.cs
Some one needs to create some indepth professinal documentation for running both linux and windows dedicated servers.