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Not an expert on this, but see e.g. this thread on JRebel forum for generating a configuration including submodules. You can also always manually add all the source paths etc. if you prefer.
JRebel for Vaadin works with Vaadin applications and you get the license key through Vaadin Pro Account but it also keeps your other classes updated so you get all the benefits of the separate version of JRebel when working on a Vaadin application.