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The version of MirrorApplication for metadata repositories and the version for artifact repositories treat the "-append" flags inconsistently. By default the artifact repository version will delete all preexisting artifacts before mirroring unless the "-append" argument is found. By contrast, the metadata repository version appends the metadata by default. The metadata version doesn't even look for the "-append" argument. See bug 247214 for more information.
Created attachment 113168 [details] Added code to handle "-append" arguement Code is pretty much taken straight from the artifact.repository MirrorApplication.java I ran the patch through my metadata test cases and they all passed.
Released to HEAD with minor changes including making the artifact repo mirroring consistent as well.