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Can I use an ANT-fileset to select files for JUnitDoclet?

Yes. Since version 1.0.2 some bug that made it more difficult is removed. But be aware, if you don't pass in packages you don't get TestSuites. ANT-filesets are sets of files, so you will end up with TestCases only. This is not as bad as it may seem, since you can use the <batchtest> of the JUnit integration with ANT to execute all your tests.