In Eclipse, go to Project / Properties menu. Go to Google / App Engine / ORM setting. It probably is set to src/ (using this setting DataNucleus puts all class files on its classpath). Instead restrict the folders (or patterns) to just the folders or file name patterns for your files that need enhancing. Hopefully, you've put them in one or just a couple of packages or named them with a common naming scheme so the fix is then trivial. Hope it helps.
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