In the modular-requestfactory archetype, proxies and request contexts in 'shared' reference domain objects and services in 'server' by name (using @ProxyForName and @ServiceName), so you cannot use the annotation processor when compiling the shared interfaces, you have to do the processing in 'server', either using the ValidationTool (as done in the Maven build), or possibly calling the annotation processor on the RequestFactory interface compiled class (I don't know of any build tool, besides low-level ones like Ant, or IDE that allows this).
I don't know how to set things up in Eclipse with WTP, but you can launch and debug the server code by using Run as… / Debug as… → Maven… to run the equivalent of the "mvn tomcat7:run" that you'd run from the command-line.