reorganize files in engine, biology, and a few others

scripts/development/run-argonnite-1-28.sh
39m1.769s

This is +5 minutes just by changing file names

Link: https://github.com/GeneAssembly/biosal/issues/354
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
set thread affinity

34m49.418s

Link: https://github.com/GeneAssembly/biosal/issues/352
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>