Merge pull request #1775 from RosettaCommons/rhiju/declare_chemical_bond_at_loop_cutpoints
declare chemical bond when CUTPOINT_UPPER and CUTPOINT_LOWER are assigned at a chainbreak
Only tests that change are ones that failed before (cppcheck; thermal_sampler in debug_release), and bridge_chains gets a much lower energy due to absence of repulsion between the atoms bonded across the chainbreak.