create a snakemake file for running both pipelines all at once

[aryarm]

The prepare and classify pipelines are split into two different pipelines in case the user wants to tweak the output of the prepare pipeline before feeding it to the classify pipeline.

But the majority of users won't want to do that. It'll be more convenient for them if there's one single Snakemake file that can run both pipelines at once. This should be easy to do if I just import the rules defined in Snakefile-prepare and Snakefile-classify into the big Snakemake file.

Also, consider re-organizing the files in the repository to match Snakemake's recommendations. This might be especially useful if we ever output figures in a Snakemake report or Jupyter notebook (see issue #7).