Created attachment 822734 [details]
simple reproducer

Description of problem:
Even if configure a ear-subdeployments-isolated attribute with jboss-deployment-structure.xml [1] and put under a <EAR>/META-INF directory, the isolation flag will be overwritten by the sub-system configuration [2].

[1] jboss-deployment-structure.xml
<jboss-deployment-structure>
<ear-subdeployments-isolated>true</ear-subdeployments-isolated>
</jboss-deployment-structure>

[2] org.jboss.as.ee.component.deployers.DefaultEarSubDeploymentsIsolationProcessor.java
53#    @Override
54#    public void deploy(DeploymentPhaseContext phaseContext) throws DeploymentUnitProcessingException {
55#        final DeploymentUnit deploymentUnit = phaseContext.getDeploymentUnit();
56#        // we only process .ear
57#        if (!DeploymentTypeMarker.isType(DeploymentType.EAR, deploymentUnit)) {
58#            return;
59#        }
60#        final ModuleSpecification moduleSpecification = deploymentUnit.getAttachment(Attachments.MODULE_SPECIFICATION);
61#        // set the default ear subdeployment isolation value
-> 62#        moduleSpecification.setSubDeploymentModulesIsolated(earSubDeploymentsIsolated);
63#    }


Version-Release number of selected component (if applicable):
6.1.1
6.2.0 Beta1 (AS 7.3.0.Final-redhat-8)

How reproducible:
Always

Steps to Reproduce:
1. Run EAP 6 server (using a standalone.sh)
2. Depoloy a SimpleEAR.ear (This application sets a ear-subdeployments-isolated=true with META-INF/jboss-deployment-structure.xml).

Actual results:
3. You can deploy it.

Expected results:
4. Stop EAP 6 server.
5. Modify a standalone.xml
- Add following.

        <subsystem xmlns="urn:jboss:domain:ee:1.1">
            <ear-subdeployments-isolated>true</ear-subdeployments-isolated>

6. Run EAP 6 server (using a standalone.sh)
7. You cannot deploy the SimpleEAR.ear for NoClassDefFoundError or ClassNotFoundException.

I think that the result of Step 3 must be the same as this.