Remove bogus DTD declaration from web.xml

The web-app element requires version 2.4 of the Java Servlet specification
while the DTD points to version 2.3. This confuses some app servers and e.g.
GlassFish 3.1 reports the following error and refuses to deploy the
application:

Error occurred during deployment: Exception while deploying the app [coberturaFlush] : org.xml.sax.SAXParseException: Attribute "xmlns" must be declared for element type "web-app".. Please see server.log for more details.

I don't think there even is a DTD for version 2.4 anymore and removing the
2.3 DTD declaration fixes the issue.
Bring web.xml elements into correct order

The 2.4 web-app XML schema is strict about the order of some elements
in the web.xml. Put the elements into the correct order.
Remove duplicate web.xml file

The file that actually gets bundled is in src/main/resources.
Do not add dependencies to web app manifest classpath

No dependencies are needed except for cobertura.jar. The classpath manifest
entries will trigger errors like this when deploying to GlassFish 3.1:

|WARNING|glassfish3.1.1|org.apache.jasper.runtime.TldScanner|_ThreadID=24;_ThreadName=Thread-2;|PWC6351: In TLD scanning, the supplied resource file:/opt/glassfish3/glassfish/domains/domain1/applications/lib/hamcrest-core-1.3.jar does not exist