Merge pull request #251 from RosettaCommons/kalekundert/fix_integration_tests
Fix three integration tests that I accidentally broke a while back: favor_native_residue, hotspot_graft, and place_simultaneously. Three tests remain broken: antibody_graft, pocket_suggest_targets, and mpframework_syndock. The former two were broken before my original commit and the latter one was broken after, so I won't be doing anything about those.
The instabilities in the KIC_with_fragments test are also probably related to my original commit, since the instabilities started around then and my commit made a lot of changes to that code. So my next goal will be to track down that bug.