The rule created for jboss-deployment-structure.xml (WINDUPRULE-97, WINDUPRULE-99) is insufficient. The rule expects that the XML file will use one of the supported namespaces (urn:jboss:deployment-structure:1.*), but it turns out that EAP processes the file just fine even if it doesn't specify a namespace.

I.e., this is supported:

<jboss-deployment-structure xmlns="urn:jboss:deployment-structure:1.2">
  ...
</jboss-deployment-structure>

But this is supported as well:

<jboss-deployment-structure>
  ...
</jboss-deployment-structure>