GoJara 2.0 is out, mainly a stability & performance update.
For updating to 2.0 please stop OF server, remove gojara.jar / gojara folder and put the new jar in plugins directory. From 2.0 on unloading works fine and there should be no problems anymore with updating it from the OF-Console plugin panel.
For whole changelog see http://issues.igniterealtime.org/browse/OF-635