Hi Benjamin,
I'm not sure what can you do to work around IntelliJ bug, but you shouldn't mention a jar under lib/ in the application.xml at all: <java> means an app client jar.
If you have a PU in an EJB jar, a war file won't "see" it - that PU will be local to that EJB jar. To be able to share a jar with PU in it, it need to be placed into an ear file lib/ directory and as such have no refs in the application.xml.
Regards,
-marina
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