Clean up generate-workflow.py after paper submission

[mattmccutchen-cci]

#33 added a ton of duplicate code to generate-workflow.py for different versions of the source code for each benchmark (original, manual port, C3 reversion of manual port). When we have time, we should clean this up (unless we decide to delete the extra versions anyway once we're done with the paper).

[mattmccutchen-cci]

It looks like much of the duplicate code was removed in #36. However, there are still other changes that were made without code review and should be cleaned up now.