No longer use temporary files when doing the "Quick setup" for a pipeline
Currently, when doing the Quick Setup of a knope/heterodyne pipeline, it creates temporary files for b any par files that get generated and for the associated equivalent configuration file. This should be changed to actually create the files in a specific location within the setup base directory. This makes three configuration file useable for other things (like #110 (closed)) and will also stop par files being generated multiple times.