You don't say, but I assume your problem is with Eclipse JPA (Dali) and its understanding of persistence.xml.
Eclipse Dali does have issues with this mechanism and im currently not aware when/if they will support jar-file properly.
since i'm curious on this too i've opened this thread: http://www.eclipse.org/forums/index.php/m/897882/#msg_897882 at eclipse dali forums.
Feel free to give your usecase/example/issues over there too. Thanks.
Max thank you for the additional information. I did not have enough information to identify Dali as the culprit. So now i know that I am keen to see if/when dali will provide the appropriate support and will folow your trail over on eclipse.