The very specific answer depends on what you're doing exactly, but I already answered this in my last post. If you've called "run" in one
thread, then to stop the engine, you need to call "halt" in another thread. Simple as that.
The simple command-line client jess.Main provides no way to do this from the command-line. Once you call run, you have to wait for it to stop on its own.
I've never touched JBuilder, so I can't give any JBuilder-specific answers.