It seems you have deleted the generated xml directory for the whole server (not just for your application) which includes the generated xml directory for the system apps (e.g. MEJBApp).
As we don't allow user to redeploy system applications, you would have to reinstall your appication server to get the system applications back.
If you don't want to re-install server for some reason, you can try to re-install server on another machine, and then copy the generated/xml directory back. But it's safer to just reinstall server at this point.
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http://forums.java.net/jive/thread.jspa?messageID=372550