Played with this today. Am able to reproduce on Felix w/o Arquillian, but can not reproduce on Karaf. Best guess is that Felix was working solely due to TCCL being set to the aggregate class loader. Without it, "bad things happen", but I'm not quite sure exactly what causes it.
Realistically, Arquillian + Felix has always been a gigantic pain in the ass. Since Arquillian has apparently deprecated support for embedded Karaf (still support remote and managed, but they'd require us to deploy our own instance of Karaf), it might be worth going back to Pax Exam. Karaf is desirable – stable, remote debugging, etc.
A few things I needed to change while debugging: https://github.com/hibernate/hibernate-orm/compare/master...brmeyer:HHH-9699
For now, don't let this hold up the 5.0.0.Final release...
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