The Command Line Argument Helper now works as intended and automatically modifies the command line as the user checks and unchecks options that are available. Also added a user-friendly dialog box for un-configured first time use. Also added JAVADOCS to release file with links in the About.html file.
The first alpha release isn't very feature-rich, but it does allow the user to open up two local Eclipse files in an external diff tool. More features will be added soon.