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I take the same database, seam-gen both versions, then diff the output directories.
I actually keep around a couple of old copies of that output (i.e. directories), named uniquely.
I'm using DiffDog, which is nice because of how it is smart about XML.
Just to clarify above post, I do both new-project and generate-entities for the old and the new version of Seam, then compare old and new version.