Initial work on parsing the command line with a standard parser.
Mostly converted command line parser.  Just need to run checks.
Renamed ModelerCommandOptions to CommandOptions.
Completed changing over the command line parsing system.
It is now possible to run all the major functions from the command line as well as the UI.
Merge pull request #6 from DJGosnell/commandline-parser

Merging Commandline parser branch.