Eclipse is a monstrous piece of pretentiously well-designed platform.
Eclipse native dependency is osgi, not Maven. Maven and eclipse integration have lots of room for improvement - but how much more Eclipse is willing to accommodate the efficiency of Maven is questionable because OSGI is their own backyard. That does not explain very much your problem - but that is the fundamental cause of your problem because the disconnect makes it hard for any non-OSGI framework to give the end-programmer a satisfactory programming experience.
This happens frequently when you create a project and then turn it into MAven. Or you create a Maven project and turn it into a web project. Is it Maven's fault? Of course it is - because Eclipse does not make it easier for non-OSGI to play with it. Eclipse does not make it easier for Ant to auto-build Eclipse projects. And even though Eclipse has no means to allow build scripts that you could submit to your OS scheduler, it does not make it easy for Ant or Maven.
Perhaps, eclipse should abandon OSGI and just work with Maven hand-in-hand to jointly improve our situation. OTOH, Maven is a framework where their creators would like it to be a generic build/dependency system that is as generic as possible and not locked into Eclipse. On the other other other hand, Eclipse wants to be as "generic" a development platform as possible and not get locked into Maven. So the two perceptions striving for generic orthogonality is completely non-orthogonally aligned. Eclipse needs to rethink their raison d'etre.
So, what you have to do is, search for the source folders that got neglected and right click on it to use them as source in the buildpath properties. Inspect your web.xml to ensure that the greetings rpc remote service is listed.