The fix for JANDEX-12 was applied so that jars were not deleted when -m was used on a system where the temp directory is on a different file system.

The change has a problem which makes it not work at all as far as I can tell. JarIndexer.createJarIndex() calls copy() before the ZipOutputStream (out/zo) has close() called on it. Although flush() is called, that does not write out the zip metadata trailer (only close() or finish() do), resulting in corrupt files.