Merge pull request #432 from RosettaCommons/JWLabonte/clean-up
Code Clean-Up: Removing Large Chunks of Blank Lines & Commented-Out Code
This merge removes a couple tens of thousands of blank lines or commented out code from Rosetta.
It also corrects some common Doxygen errors.
See the pull request for more details.
All unit tests pass.
jscore and score_jd2 integration tests change because they output a line number.
The Windows PyRosetta build was already broken.
:rat: