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I get errors like this when attempting to run unit tests under App Engine SDK 1.2.8. The unit tests pass under SDK 1.2.6 using the same code.
“Class com.foo.bar.BaseClass does not seem to have been enhanced. You may want to rerun the enhancer and check for errors in the output”
A class which extends BaseClass IS persisted, but has the proper annotations, etc.
A thread on GAE support group shows other reports of the same issue and links to a release-candidate version of ORM 1.0.4 which fixes this and another related bug: Support Thread
My errors were fixed by installing the ORM RC using the method provided in the GAE support wiki.
Thanks to Max Ross @ Google for delivering a fix for the problem quickly.