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As for why this does not fail in the test suite, thats easy. Apparently our test suite does not define the exact combo of mappings that cause this
Table#cleanseUniqueKeyMap is specifically intended to cleanse extra cruft created by the current annotation processor. So most likely we just do not have a combination of entities and relations that trigger this extra cruft in the test suite atm.
Guenther, or anyone else, would really like to get a simplified test case reproducing this so that we can get this added to the testsuite.