The quickstart helloworld-osgi cannot be deployed to EAP version 6.2.1.CP.CR3. This quickstart (the produced jar) can be deployed on EAP 6.2.0.GA without any issues. 

How to reproduce:
Follow instructions in README.md in the helloworld-osgi quickstart. The build of the application can be completed without problems. However, the deploy (even manual one), fails with the following exception:


14:35:09,638 INFO  [org.jboss.as.server.deployment] (MSC service thread 1-8) JBAS015876: Starting deployment of "jboss-helloworld-osgi.jar" (runtime-name: "jboss-helloworld-osgi.jar")
14:35:09,720 INFO  [org.jboss.osgi.framework] (MSC service thread 1-5) JBOSGI011006: OSGi Framework - 2.1.0.Final-redhat-1
14:35:09,864 ERROR [org.jboss.msc.service.fail] (MSC service thread 1-5) MSC000001: Failed to start service jbosgi.BootstrapBundles.INSTALL: org.jboss.msc.service.StartException in service jbosgi.BootstrapBundles.INSTALL: JBAS011955: Failed to process initial capabilities
	at org.jboss.as.osgi.service.BootstrapBundlesIntegration.start(BootstrapBundlesIntegration.java:160)
	at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1811) [jboss-msc-1.0.4.GA-redhat-1.jar:1.0.4.GA-redhat-1]
	at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1746) [jboss-msc-1.0.4.GA-redhat-1.jar:1.0.4.GA-redhat-1]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) [rt.jar:1.7.0_04]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) [rt.jar:1.7.0_04]
	at java.lang.Thread.run(Thread.java:722) [rt.jar:1.7.0_04]
Caused by: org.osgi.framework.BundleException: JBOSGI010318: Cannot get manifest from: vfs:/home/jkudrnac/jboss/jboss-eap-6.2.1.CP.CR3/jboss-eap-6.2/bundles/system/layers/base/org/jboss/as/osgi/configadmin/main/jboss-as-osgi-configadmin-7.3.0.Final-redhat-14.jar
	at org.jboss.osgi.spi.BundleInfo.<init>(BundleInfo.java:138)
	at org.jboss.osgi.spi.BundleInfo.createBundleInfo(BundleInfo.java:110)
	at org.jboss.as.osgi.service.BootstrapBundlesIntegration.getDeploymentFromURL(BootstrapBundlesIntegration.java:285)
	at org.jboss.as.osgi.service.BootstrapBundlesIntegration.getInitialBundleDeployment(BootstrapBundlesIntegration.java:241)
	at org.jboss.as.osgi.service.BootstrapBundlesIntegration.start(BootstrapBundlesIntegration.java:156)
	... 5 more
Caused by: java.util.zip.ZipException: error in opening zip file
	at java.util.zip.ZipFile.open(Native Method) [rt.jar:1.7.0_04]
	at java.util.zip.ZipFile.<init>(ZipFile.java:214) [rt.jar:1.7.0_04]
	at java.util.zip.ZipFile.<init>(ZipFile.java:144) [rt.jar:1.7.0_04]
	at java.util.jar.JarFile.<init>(JarFile.java:152) [rt.jar:1.7.0_04]
	at java.util.jar.JarFile.<init>(JarFile.java:116) [rt.jar:1.7.0_04]
	at org.jboss.vfs.spi.JavaZipFileSystem.<init>(JavaZipFileSystem.java:94)
	at org.jboss.vfs.spi.JavaZipFileSystem.<init>(JavaZipFileSystem.java:81)
	at org.jboss.vfs.VFS.mountZip(VFS.java:386)
	at org.jboss.vfs.VFS.mountZip(VFS.java:410)
	at org.jboss.osgi.vfs30.VirtualFileAdaptor30.ensureMounted(VirtualFileAdaptor30.java:321)
	at org.jboss.osgi.vfs30.VirtualFileAdaptor30.getMountedChild(VirtualFileAdaptor30.java:304)
	at org.jboss.osgi.vfs30.VirtualFileAdaptor30.getChild(VirtualFileAdaptor30.java:201)
	at org.jboss.osgi.vfs.VFSUtils.getManifest(VFSUtils.java:71)
	at org.jboss.osgi.spi.BundleInfo.<init>(BundleInfo.java:133)
	... 9 more

14:35:10,083 ERROR [org.jboss.as.server] (DeploymentScanner-threads - 1) JBAS015870: Deploy of deployment "jboss-helloworld-osgi.jar" was rolled back with the following failure message: 
{
    "JBAS014671: Failed services" => {"jbosgi.BootstrapBundles.INSTALL" => "org.jboss.msc.service.StartException in service jbosgi.BootstrapBundles.INSTALL: JBAS011955: Failed to process initial capabilities
    Caused by: org.osgi.framework.BundleException: JBOSGI010318: Cannot get manifest from: vfs:/home/jkudrnac/jboss/jboss-eap-6.2.1.CP.CR3/jboss-eap-6.2/bundles/system/layers/base/org/jboss/as/osgi/configadmin/main/jboss-as-osgi-configadmin-7.3.0.Final-redhat-14.jar
    Caused by: java.util.zip.ZipException: error in opening zip file"},
    "JBAS014771: Services with missing/unavailable dependencies" => [
        "jbosgi.PersistentBundles.INSTALL is missing [jbosgi.BootstrapBundles.COMPLETE]",
        "jbosgi.internal.framework.INIT is missing [jbosgi.PersistentBundles.COMPLETE, jbosgi.BootstrapBundles.COMPLETE]"
    ]
}
14:35:10,092 INFO  [org.jboss.as.server.deployment] (MSC service thread 1-1) JBAS015877: Stopped deployment jboss-helloworld-osgi.jar (runtime-name: jboss-helloworld-osgi.jar) in 10ms

Looks like the OSGi subsystem is not using the patched version, but the original one, which was made unusable by patching mechanism. 
[jkudrnac@jkudrnac jboss-eap-6.2]$ find . -name jboss-as-osgi-configadmin* 
./bundles/system/layers/base/org/jboss/as/osgi/configadmin/main/jboss-as-osgi-configadmin-7.3.0.Final-redhat-14.jar
./bundles/system/layers/base/.overlays/layer-base-jboss-eap-6.2.1.CP/org/jboss/as/osgi/configadmin/main/jboss-as-osgi-configadmin-7.3.1.Final-redhat-2.jar