Make coberturaFlush web app deployable to GlassFish 3.1 and other containers that strictly enforce the Servlet spec

* Make web.xml compliant with Servlet 2.4 spec.
* Remove duplicate web.xml.
* Remove non-required libraries from manifest classpath.

All unit tests pass after these changes and coberturaFlush.war deploys cleanly to GlassFish 3.1.