I think that says something bad about your deploy tool, but one way around this problem is to build up your manifest.mf file by hand and use the zip task instead of the jar task. All a JAR is is a zipfile with a manifest in it, so the JAR task adds one for you.
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Thanks for the reply. Unfortunately the deploy tool is from SAP.. and I cannot change it in any way!
I made the change to the build.xml like you suggested:
and believe it or not it, it still added the ANT header's to the resulting Manifest file. I believe anything that's added as meta-inf/manifest.mf, be it with the jar or zip task, is still modified by Ant. Perhaps there is another way to manually add a file using zip?