This is not allowed:

   <when>
           <not>  <xmlfile public-id=".*JBoss.+DTD Java EE.+5.*"/>  </not>
           <xmlfile matches="//*[local-name()='jboss-app']" in="jboss-app.xml"/>

The <xmlfile> has to be wrapped in <or> or <and>.

There's no reason for that wrapping, except for the technical ones - XSD not allowing it, and maybe the implementation.

See https://github.com/windup/windup/blob/master/config-xml/schema/windup-jboss-ruleset.xsd#L381-L410