improved exception handling (fail to open files)

refs #12
Merge branch '#12-FileSafety'
removed commend in stdafx.h/cpp
removed reference to unneeded exception variable e to get rid of warnings
refactored for clarity and added trivial things for getting rid of warnings.
fixed a quick bug resulting in failure even though file opening in successful.

resf #12
Changed Usage text.
displays USAGE if incorrect combination of inputs is detected.

refs #9
Merge branch 'dev'