I like it to be as simple as possible. The first option is easier. Is
unwrapping the Hibernate session from EMF and setting it in JNDI would be
done in Java code not xml files?

But I don't see how is this going to work, because when app is deployed the
EMF will be set. So I have to bind the session factory in JNDI when EMF is
set. Right?

Could you provide more details place? Some code will help and JNDI value to
bind sesstion factory with.

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