changed the make_file to allow the user to just run karrot instead of the python program pipe stuff. I am trying to allow a user to run an a.out file but there is a problem in that python does not like assumeing that the same program will create an a.out file. So right now if you do not have an a.out before running karrot run (karrot file). Will talk with dr chappell about this tommrow to see if we could come up with somthing