Improving Snakemake clean rule

[agitter]

Our Snakemake workflow has a clean rule that currently removes the entire output directory. We could provide more fine-grained options about what to clean. One would still be to clean all and remove the entire output directory. However, we could also clean only the intermediate output files like the prepared input data, raw pathway ouput files, and unpacked sif images (see #145 (comment)). That would keep files like the logs, visualizations, summaries, and standardized pathway files.