Merge pull request #1259 from RosettaCommons/JWLabonte/sugars/branching
Post-ChemicalXRW: removing the -read_pdb_link_records option
LINK records are now read always.
All unit tests pass.
Integration test changes expected where options have been changed.
Note that the C-terminal_conjugation patch causes a bug in some unit tests, so it has been commented out of patches.txt until the bug has been squashed. In the meantime, it can be included by the option system.