IsisPreferences was modified so TerminalOutput=On. Many app tests needed to be...

IsisPreferences was modified so TerminalOutput=On. Many app tests needed to be modified to work with this change. Pipeline is still failing. Fixed #2050.

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/trunk@5750 41f8697f-d340-4b68-9986-7bafba869bb8