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There are numerous post-install steps described in: http://dev.eclipse.org/viewcvs/indextech.cgi/~checkout~/org.eclipse.ajdt/plugin s/org.eclipse.ajdt/releaseNotes/readme.html?rev=HEAD&content-type=text/html These should be autmated. Where user input is required for automatic configuration a wizard should gather it before updating the workbench settings.
Julie has fixed this for 1.1.1
updated target milestone to 1.1.4