http://www.eclipsezone.com/eclipse/forums/t53459.html
Basically run it with:
-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=1044
The application, at launch, will wait until you connect from another source.
so the CLI command will be:
java -jar yourJarFileName.jar -Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=1044