Updated documentation and formatting. Moved call to set output cube to top of...

Updated documentation and formatting.  Moved call to set output cube to top of main() method to make sure user preferences are checked before computations are performed.

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/trunk@208 41f8697f-d340-4b68-9986-7bafba869bb8