Using appengine modules implies creating dynamic web application instead of the usual appengine web application project. Cloud endpoints work well with the usual appengine Web A
The solution to this case is within François POYER answer, but here is a version with no maven assumed.
If you are using WTP to create and manage your appengine application and EAR:
If you do not see Google App Engine WTP and you only see "Google", its likely you have not selected the Java EE perspective.
You do not have to use maven for this, simply use WTP to create and manage your EARs and appengine applications.