Merge pull request #89 from RosettaCommons/kylebarlow/warnings
Turn on Clang -Wall in scons and remove associated warnings
Currently, the scons clang build is an outlier that does not have -Wall and other flags
It now matches the Cmake clang build and g++ scons build.
This required fixing Clang warnings that hadn't been fixed yet,
and which were causing problems for Ninja builders.