Not a Processing Implementation question, moved.

There is a command line interface, but last time I checked, it was broken.
But indeed, exporting it should work. All it does is to generate a jar file with the needed parts, and to run it with a small launcher. What issue have you with the serial library?
No need to sign the jars outside of applet usage.

Oh, sorry for wrong placement, thank you for moving the question.

The issue was that the applet form was not communicating with the serial port, while opening the main jar with java resulted in an error (main class ...)
I found out about "Export Application", which works fine! :)

Applets need to be signed to work with hardware...
And don't worry about misplacement, I do that (moving threads) all the time. Although it would be nice to read the section descriptions... (if they are not clear/ambiguous, don't hesitate to give feedback).