Use a different temp directory for each NetMHCcons instance, moved

mutate from epitopes into immuno, parse stdout of NetMHCcons instead of
xls files (to avoid clobbering hardcoded output file path)
It seems strange to me that passing in (True, False, True) would automatically become (False, False, True). But rather than making this unnecessarily complicated, can we just leave the choice of supress_stdout = False to the caller? (Since that's what the method signature seems to imply?)