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Whether or not the name of the file is specified in the arguments, moxy generates its own file name based on the namespace. Even then, it won't overwrite the file if it exists, it generates a new name. This causes problems in Dali, because we can't do anything with the schema post-generate. It also makes the process of regeneration cumbersome, because the user ends up with multiple similarly (incorrectly) named schemas all in the same place.
I'm not sure what didn't work before, but I'm getting what I *think* should be the correct behavior. Closing.
The Eclipselink project has moved to Github: https://github.com/eclipse-ee4j/eclipselink