I suggest you look at M2T-JET to generate not only the Java files, but the project, any necessary folders and any other resources you need. One of those resources would be a jardesc file which is used by the JDT to persist jar export options. You can play around with those options to define the jar and export, then generate the jardesc file along with the other generated resources.
M2T-JET can be invoked programmatically, so once that single invocation generates your entire project, your plugin can make the call to the JDT to export the jar using the jardesc file.