The Jar files and the JavaBE.ini are not included in the Agentry Editor, and would need need to be moved over by themselves.
Starting SMP 3 SP02, the Editor can support Zip publishes which you can tell the editor to grab other files and include them within the Application in a Zip file that can then be upload to the server.
and the reason why I say jar files, because there is more then one jar file that need to be moved, and also 2 dll files that are needed for sapjco.
Stephen