Merge pull request #1963 from RosettaCommons/roccomoretti/enable_CIF
Attempt to (re)enable mmCIF input on JD2
Update 'PDB'JobInputter to use the auto-detection logic and update the auto-detection logic.
Add usage of mmCIF input to integration tests to catch if we break it (again).
Large number of cosmetic integration test changes expected, as an additional diagnostic line has been added to PDB loading.