- All the workflow to identify rec. ret. gene
  families is now called inside fc_wgd, at the
  same place where the standard pipeline calls
  blast and mcl, and replaces their use.
- The workflow code is still stored in a module
  aside, extend_orthogroups.py

"plot-paralogs" command generates the "rate_adjustment/species" directory if the directory doesn't exist (i.e. it has been deleted), avoiding that the code crashes.