The problem with jsps not displaying correctly was due to the servlet-mapping elements being mapped to an AbstractMappedMetaData type. This means that for a fragment like:
<!-- The mapping for the JSP servlet -->
<servlet-mapping>
<servlet-name>jsp</servlet-name>
<url-pattern>*.jsp</url-pattern>
</servlet-mapping>
<servlet-mapping>
<servlet-name>jsp</servlet-name>
<url-pattern>*.jspx</url-pattern>
</servlet-mapping>
only the last mapping for the "jsp" servlet was in the map. Only types that have a uniqueness constraint such as the servlet type can be modeled as AbstractMappedMetaData. The servlet-mapping elements need to be modeled as a list of ServletMappingMetaData rather than a map. Just an FYI in case you find that repeated data is being lost.
