JBoss EAP Cumulative Patch Releases breaks my project build path on JBoss Developer Studio (JBDS)

Issue

• My projects in Red Hat JBoss Developer Studio (JBDS) fail to build once I upgraded my build patch server runtime to JBoss EAP 6.2 CP01 (EAP 6.2.1)
• I cannot build code that will run on RedHat JBoss EAP because of changes for new patch process (corrupt JAR's)
• I get errors on my project build patch similar to the below

Archive for required library: '/home/mmusaji/JBoss/jboss-eap-6.2.1/modules/system/layers/base/org/picketbox/main/picketbox-infinispan-4.0.19.SP2-redhat-1.jar' in project 'HelloWorld' cannot be read or is not a valid ZIP file