Updates that implement stepwise monte carlo for proteins, on the way to unified SWM implementation for RNA/protein complexes (from rhiju/swm_general branch). Several additional fixes, including restoration of swa_rna_gagu_17 and swa_rna_gagu_20 integration tests, and addition of some swm_protein integration tests. Checked integration tests -- besides changes in RNA, SWA, and SWM tests, some cosmetic changes due to change in fa_standard patches and addition of TAUTOMER propery to HIS_D residue type. On my mac I also see a late change in an antibody test, which seems like a floating point deviation.