Merge pull request #58 from RosettaCommons/tjacobs2/fix_link_residues
This commit fixes a few issues I ran into while using LinkResidues task operations.
In particular, it seems residues were being linked to themselves (which will always
cause an assert failure when run in debug mode). Also, added some robustness to the
addition of residues after creating links. Previously, this would cause an index-out-of-bounds error.
My fix might cause undesirable behavior if residues are added that change residue-numbering (e.g. add rotamer links, create a new residue with resid = 1, repack). Is there a better way to implement this change?