Merge pull request #714 from RosettaCommons/aleaverfay/prebeauty_cleanup
Merging branch aleaverfay/prebeauty_cleanup into master (pull request #714).
Modifying files ahead of beautification that contain un-scoped if blocks
and other statements all on a single line. The beautifier now flags such
lines as sources of possible bugs. However, it demands that if you want
to put several statements on one line, that you should scope the if block.
This commit goes through all the cases in the code that the beautifier
flags and scopes them appropriately.