Polished main paper and appendices after a full re-read

In preparation for the submission of the revised manuscript, I went through
the full paper and appendices one last time. The second appendix (reviewing
existing reproducible solutions) in particular needed some attention
because some of the tools weren't properly compared with the criteria.

In the paper, I was also able to remove about 30 words, and bring our own
count (which is an over-estimation already) to below 6250.

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