I've deployed a duplicate tomcat stack on a virtual server in order to debug the issues so far. These include XEP and Saxon8 most importantly, but also includes automounting of users homedir/webapps directory (if present) to discover cocoon apps.

Another item on the list is building, installing and figuring out the XML Differencing module (see here).

tomcat's conf file server.xml allows you to turn off unpacking of WAR files and autodeploy of webapps. I've disabled this on my localhost install.

The current issue is that building and installing xep is apparently successful, but the sitemap refuses to load with a config error at the xep stanza. The error is described as
org.apache.cocoon.ProcessingException: failed to load sitemap from...{location} at [ConfigurationException] - {location}/sitemap.xmap:323:44

The problem is in the build. My current build only produces a XEPSerializer.jar with a manifest in it. The version on mustard has a proper tree with classes in it.

Next step: find out why this is happening and fix it.