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Java module needs to replace location chooser when N.F.T. Wizard is invoked from within its "Packages" -- see java projects UI spec, sections "Creating New folders", "Creating New files" etc. The current N.F.T Wizard implementation does not allow that.
How's that? I think this is implemented: http://www.netbeans.org/download/dev/javadoc/LoadersAPI/org/openide/loaders/TemplateWizard.html#createTargetChooser() together with http://www.netbeans.org/download/dev/javadoc/LoadersAPI/org/openide/actions/NewTemplateAction.Cookie.html should allow you to do this. Moreover your TemplateWizard.Iterator can always skip the default target chooser and provide own.