Refine guidelines and ease for iterative refinement of plot

[JustinChu]

Often some link parameters will need to be tweaked and pipeline rerun. The make file structure of the tool helps with this but requires some understanding of make files to do so without having to re-do alignments. I need to:

• Add in readme to explain how to refine plot without accidentally reusing the wrong intermediate files
• Add some parameters or change what files are removed after the pipeline is run