Bug fix. Command line improvement (now accepts .cub/.lis/.mos as specified,...

Bug fix. Command line improvement (now accepts .cub/.lis/.mos as specified, loads projects first). Documentation improvement - not done yet - references #427

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/trunk@3309 41f8697f-d340-4b68-9986-7bafba869bb8