Merge pull request #1066 from RosettaCommons/vmullig/ter_records_at_chain_ends
Post-XRW cleanup: add TER records between chains in PDB output.
This adds TER records between chains (as is the PDB standard) in PDB output. This is something that Rosetta has never done properly, but now it will. Of course, this means that every integration test that writes PDB files will fail. This is a separate pull request for that reason: it will cause many, many integration test failures.
Also, I'm removing some unneeded (and, in some cases, now-dangerous) code. I'm also moving some functions that were implemented as stand-alone utility functions into the PoseToStructFileRepConverter class, as private member functions (since they're never called from anywhere else).
The legacy behaviour can be restored with the -out:file:no_chainend_ter flag.