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JavaProjectGenerator now lets you add to the list 'javadoc' in a compilation unit, with similar semantics as for 'output'. Now the freeform project properties dialog (Output panel) should permit you to specify a Javadoc build location.
Fixed according to spec with one difference: there is no "Separate Output" checkbox. Jano, was it added intentionally? We had it there before and later removed it before 4.0 release because it does not make sense there (there is just one checkbox on Classpath panel). So I omitted it. Adding it would make logic behind UI more complicated and would require more time to impl. Fixed in: src/org/netbeans/modules/java/freeform/ui/Bundle.properties; new revision: 1.4; previous revision: 1.3 src/org/netbeans/modules/java/freeform/ui/OutputPanel.form; new revision: 1.3; previous revision: 1.2 src/org/netbeans/modules/java/freeform/ui/OutputPanel.java; new revision: 1.4; previous revision: 1.3