The gae stuff is not needed in gwt projects, in fact most of my projects use a non gae server side solution: spring, couchdb, php, rails.
Think that gwt is to produce an app to be run in a browser sending ajax requests to any server side implementation.
If your backend is java, you can take advantage of a couple of things which the gwt-server library provides and which makes that ajax easier (RPC, RF), but gwt does not provide anything for your server implementation (persistence, injection, etc), and gives you the freedom to select anything (spring, grails, gae, etc)
If your backend is not java, you have to use traditional ajax making requests and parsing the json or xml results. Gwt gives you some utilities to parsing those responses, or you could use a 3party library like gwtquery.ajax.
In the other hand you can use gae without gwt in the browser (jsp, spring-mvc, etc)
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