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I'm working off the current CVS HEAD. When using ajc to weave against a jar file a separate warning message is generated for each file under the input jar's "meta-inf" directory that is not copied across to the output jar. Depending on the input jar being weaved against, this can result in a lot of messages which might be of no interest to the user. If no -outjar option is specified (allowing the ajc output to go to the present working directory) then the messages are still emitted.
bug #44190 has changed the behaviour of the weaver so that meta-data is always copied. Warnings will still be issued for duplicate resources e.g. when multiple injars are woven into single outjar.
updating target flag to indicate inclusion in 1.2 release.