This must be the weekend that I discover obvious shit that I never knew before. The first thing that Matt said on #mobitopia after reading my PC Suite converter post below is "you didn't know that?". Doh!
So last night I was getting frustrated with a bit of server-side Java and I was like "there's got to be a way to step through this on the server... I've done it with Tomcat before." Well, yeah. Duh. It's so *ridiculously* simple to set up I'm kicking myself for not doing this over a year ago.
Simply go to the debug dialog box and add a new configuration under "Java Application" on the left, in the Main Class text box put "com.evermind.server.ApplicationServer", then in the Arguments tab, change the working directory below to the Orion directory. Finally, go to the Classpath tab and deselect the "use default classpath" checkbox, this will allow you to add an external Jar file, which will be orion.jar.
That's it. Hit "Apply" and then below click the debug button and Orion will start up within the context of Eclipse and you can step through your server-side code easily and instantly.
I can't believe what an ass I am for not doing this before. Urgh!