Merge pull request #719 from RosettaCommons/rhiju/fix_carbohydrate_patches_with_on_the_fly_residue_types
Rhiju/fix carbohydrate patches with on the fly residue types
carbohydrates integration test restored, confirmed by @JWLabonte.
All other tests pass except ones that failed before (cppcheck, 3 integration tests; the match tests, which can give different output orders).