Merge pull request #1022 from RosettaCommons/tjbrunette/fast_forward_folding
Tjbrunette/fast forward folding this code introduces code to: A. Generate a structural profile fast. B. Fix the structure of short loops. C. Score centroid models with Will's motif score term.
-The integration test errors are expected and due to the new energy functions
-Most of the new code uses an hdf5 database so there are no integration tests to protect it because hdf5 needs a different compile then is currently being done.