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The methods for retrieving a PUDataObject instance in the o.n.m.j2ee.persistence.provider.ProviderUtil class assume that there is only one persistence.xml file per project. This is incorrect since the JPA specification allows to have several persistence.xml files. See also issue 96777 desc 6 for more information.
To clarify this issue a bit: The spec allows multiple persistence.xml files in an *application*. What I had in mind was persistence units defined at the EAR level, but thinking about it now it is questionable whether that use case should (or can) be supported by the ProviderUtil. In any case, the issue is still valid for the case Andrei describes.
There are currently no clients that would need this for 6.0, so the correct priority for this is rather P3. Need to be re-evaluated when there are clients that would need this, such as the freeform projects.
Setting the TM to future as per desc3.
I guess there is no point in keeping this issue open as long as we don't plan to fix it (which we currently don't, as it would require major changes).