Ah ha, I did some more digging and I found this in the debug launch for the roboRIO
Code:
/usr/local/frc/JRE/bin/java -XX:+UsePerfData -agentlib:jdwp=transport=dt_socket,address=8348,server=y,suspend=y -jar /home/lvuser/FRCUserProgram.jar
So if i'm correct you should be able to hotswap code if you connect to the roborio over port 8348, I haven't tested it yet but I will be sure to post my results when I get into school tomorrow.