Merge pull request #384 from RosettaCommons/rpache/KIC_outer_cycles_bugfix
Loop modeling outer cycles refactoring
This commit makes perturb_outer_cycles and refine_outer_cycles the flags
to control the number of outer cycle iterations in the centroid and fullatom stages,
respectively, for all loop modeling protocols.
The default values for those two options are now being read directly from the
Rosetta options system instead of using hard-coded values.
The old loops:outer_cycles flag is now deprecated.
Cosmetic splice and antibody loop modeling integration test changes.