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See EclipseLink bug 354678. If we can get EclipseLink to set its temp loader to the real OSGi loader then all of the places where it uses its temp loader will not hurt of cause failure when running in Gemini JPA. Note that this will only work if the temp loader is not used to load any classes that EclipseLink is going to to be weaving later.
EclipseLink team is apparently fixing the bug so it doesn't look like a workaround will be needed.