As a quick follow-up, the specifying of -npa on the XJC task does in fact solve the package level annotation problem. I've opened PR https://github.com/sebersole/gradle-xjc-plugin/pull/1 for the XJC plugin we use to integrate the XJC task with Gradle. Once that has been integrated and a new release of the plugin published, I can then resolve this in the ORM build.