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It's not clear what will the role of javadoc module in new projects infrastructure. Either javadoc module will work the same way as now or project's javadocs will be part of project Resources node and generated javadoc part of project Output. Small UI spec would be great.
the description you've given -that there are resource javadocs and output javadocs -is correct. this is described in the Java Projects UI spec.
i am marking this as invalid for now. the information is already in the spec. i will add a quick note to clarify in the next revision of the document.