Reading http://confluence.jetbrains.com/display/IDEADEV/External+Builder+API+and+Plugins, it seems to say that the jps portion of your plugin should be built into a separate jar, somehow. I am working off the Haxe plugin source that was recently opensourced, but when I tell that project to "Prepare all plugin modules for deployment", it is not packaging up the plugin the same way as the way it is on the official plugin repository.
The official plugin has a haxe-common.jar, haxe-jps-plugin.jar, haxe.jar, and resources_en.jar. The thing made by 'Prepare...' seems to be a single mashed together jar of just the common, resource, and core stuff, but leaves out the jps plugin.
There's something on the above external builder page about "The plugin layout in layouts.gant should be changed to pack the module into a separate jar" but I have been unable to figure out what that means, exactly. There is no layouts.gant in the tree, and google is not helpful.