Minor edits, updated citation to published Menke+20 paper

Some minor edits were made to the paper to shorten it. In particular the
example of IPOL was removed from the main body of the paper, and we'll just
rely on the more extensive review of IPOL in the appendix. I also updated
the referee report to account for the new Appendix A that is just an
extended introduction.

Also, I noticed that the Menke+20 paper that we replicate here has recently
been published in the iScience journal. So its bibliography was updated
from the bioarXiv information to the journal information.

Also, the number of words (after removing abstract and captions and
accounting for figures) is now only printed when the project is built with
'--no-appendix'. This was done because this information is
extra/annoying/unnecessary for the case where there is an appendix.

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