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As it has been done for generic xml discoverer, in choosing the serialization to true, the result file should not be just a copy of original xml file but a xmi file serialized conforming to the MoDisco ecore definition. The same problem shall exist for ejb jar discoverer.
Issue is more an enhancement. Setting importance to P5.
For information, here is a thread on the MoDisco forum related to this problem: http://www.eclipse.org/forums/index.php/t/350944/de04b7529460e69886458a6424436d7f/