Not possible to use the modules from the modules directory for development or execution after applying a CP patch to EAP 6

Issue

• It is not possible to use the modules director for development, the jar files are corrupted.
• A ClassNotFoundException occurs after applying patch JBoss EAP 6.2 CP0x (EAP 6.2.x) for clients.

• The following information is what we found for the missing class, and we guess that the patch did not put the new file to the right places under /system/layers/base/org/jboss/xnio/nio/. In the contrary, the new files just exist under /.overlays/layer-base-jboss-eap-6.2.1.CP. So we think there is something wrong with the patching mechanism for EAP.

  # find . -name "xnio*"
  ./jboss-eap-6.2/modules/system/layers/base/org/jboss/xnio
  ./jboss-eap-6.2/modules/system/layers/base/org/jboss/xnio/nio/main/xnio-nio-3.0.7.GA-redhat-1.jar
  ./jboss-eap-6.2/modules/system/layers/base/org/jboss/xnio/main/xnio-api-3.0.7.GA-redhat-1.jar
  ./jboss-eap-6.2/modules/system/layers/base/.overlays/layer-base-jboss-eap-6.2.1.CP/org/jboss/xnio
  ./jboss-eap-6.2/modules/system/layers/base/.overlays/layer-base-jboss-eap-6.2.1.CP/org/jboss/xnio/nio/main/xnio-nio-3.0.9.GA-redhat-1.jar
  ./jboss-eap-6.2/modules/system/layers/base/.overlays/layer-base-jboss-eap-6.2.1.CP/org/jboss/xnio/main/xnio-api-3.0.9.GA-redhat-1.jar
  

• After applying a CP patch to EAP 6.2.0 the jar references for development are not valid.

• We tried to update the unpacked EAP 6.4 with the EAP 6.4.2 on Windows. Afterwards we did a diff using a tool. So it shows up that "bundles/system/layers/base/org/jboss/as/osgi/configadmin/main/jboss-as-osgi-configadmin-7.5.0.Final-redhat-21.jar" could not be opened.

• Examining the EAP 6.4.2 ZIP we found this file to be part of EAP 6.4.1 while in the EAP 6.4.2 there is "jboss-as-osgi-configadmin-7.5.2.Final-redhat-2.jar" which could be opened .
• Do you have any idea why:
  1) The file is corrupt after update?
  2) The file is not the most recent version?