I've reported three (very minor) issues to the Google App Engine issue tracker:
#1414: NullPointerException when deploying with web.xml = <web-app />
#1415: .java/.jsp files uploaded to the live environment?
#1416: Extra JAR:s being added to WEB-INF/lib/ and uploaded on each deployment
These three issues were discussed in some detail in my blog post "Deployment on GAE/J and the minimal GAE/J application".