<appengine-web-app xmlns="http://appengine.google.com/ns/1.0">
<application>your app</application>
<module>default</module>
And of course change the name to another name on your current default module.
Should be simiular in other languages as well, for 2:nd gen or flex env I don't know, probably you need
to change something in a yaml file or whatever popular these days.