module defined in jboss-deployment-structure.xml with fails to parse when annotations=true in JBoss EAP 7

Issue

• We have an EAR application with subdeployment Jars under root of EAR listed as modules under application.xml and a Jar with annotations that contained under the root folder of the EAR and we have it listed under the jboss-deployment-structure.xml as an inline module. We created the jandex and set annotations=true as per the documentation [1]

The deployment fails with missing dependencies when annotations=true is set :

10:42:56,061 ERROR [org.jboss.as.controller.management-operation] (Controller Boot Thread) WFLYCTL0013: Operation ("deploy") failed - address: ([("deployment" => "application-exception-using-dynamic-module.ear")]) - failure description: {"WFLYCTL0180: Services with missing/unavailable dependencies" => ["jboss.deployment.subunit.\"application-exception-using-dynamic-module.ear\".\"application-exception-ejb.jar\".PARSE is missing [jboss.module.service.\"deployment.application-exception-api\".main]"]}

[1] https://access.redhat.com/documentation/en-us/red_hat_jboss_enterprise_application_platform/7.0/html/development_guide/class_loading_and_modules#add_an_explicit_module_dependency_to_a_deployment

• The jboss-deployment-structure.xml file looks like:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<jboss-deployment-structure xmlns="urn:jboss:deployment-structure:1.2">
  <sub-deployment name="application-exception-ejb.jar">
    <dependencies>
       <module name="deployment.application-exception-api" annotations="true"/>
    </dependencies>
  </sub-deployment>
  <module name="deployment.application-exception-jds.ear.application-exception-api.jar">
    <resources>
     <resource-root path="application-exception-api.jar"/>
    </resources>
  </module>
</jboss-deployment-structure>

• the application.xml file looks like:

<?xml version="1.0" encoding="UTF-8"?>
<application xmlns="http://java.sun.com/xml/ns/javaee"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/application_6.xsd"
  version="6">
    <module>
        <ejb>application-exception-ejb.jar</ejb>
    </module>
</application>

• the ear-subdeployments-isolated property is set to true under the EE subsystem in standalone*.xml/domain.xml