Not sure if this is the right place to raise an issue on this docomentation, but I will do so to at least capture to issues.

To use a custom Dockerfile, the runtime in the app.yaml file must be changed from java to custom

The documentation says that if you wish to use a custom Dockerfile, you must build the war and put it in the source directory next to app.yml. This is not the case, rather the war is already build for you and is placed in target/appengine-staging. A dockerfile as follows may be used:

FROM gcr.io/google_appengine/jetty9 ADD projectname-version.war $JETTY_BASE/webapps/root.war 

where projectname and version are from maven (it would be really good if maven property expansion could be done on the Dockerfile when copied to target!!!)