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Just a suggestion: It isn't immediately obvious to me why there needs to be a .jardesc file format, when it seems to me that ant will do all and more. The immedidate advantage for me with ant build.xml files is that they can be configured to build a jar file out of all the .class files in the project. jardesc files need to be updated every time I add or remove .java files from the project. Perhaps this is possible with .jardesc files, but it isn't immediately obvious. My solution: dump .jardesc and only learn ant build.xml files.
Moving to JDT - this is a feature request for JDT, not ANT.
Daniel, can you comment on the difference of the Jardesc file and ant files. And of course you can write your own build.xml file and use that one to export a Jar instead of using the export wizard.
That's true you could do more with the ant file (e.g. exclusions) and that's exactly the problem, e.g. what would you expect the wizard to do if the user edits the generated ant (build.xml) file and then reopens the wizard? One possibility could be an action which allows to generate a build.xml either directly from the wizard or from an existing .jardesc file. As you can see in bug 3609#c2 we already discussed this.
*** This bug has been marked as a duplicate of bug 117762 ***