I created a mainly empty dynamic web project in eclipse.
It has
The web.xml is
I think this is a bug in Tomcat. I filed a bug report but they claim it works as designed. Tomcat has 3 modes of deployment: Directory, WAR and Context Fragment. In your case, it gets confused when reloading.
Here is the sequence leading to the error,
If you only change the XML in META-INF, everything should work for you.