Fabric GIT Repo Corruption - EOFException: Short read of block

2016-05-30 08:34:56,626 | ERROR | Thread-66        | fabric-git                       | ?                                   ? | 85 - io.fabric8.fabric-git - 1.0.0.redhat-429 | [io.fabric8.datastore(38)] The activate method has thrown an exception
io.fabric8.api.FabricException: Failed to start GitDataStore:
	at io.fabric8.git.internal.GitDataStore.activateInternal(GitDataStore.java:212)
	at io.fabric8.service.AbstractDataStore.protectedActivate(AbstractDataStore.java:115)
	at io.fabric8.git.internal.CachingGitDataStore.activate(CachingGitDataStore.java:103)
	at sun.reflect.GeneratedMethodAccessor17.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)[:1.7.0_75]
	at java.lang.reflect.Method.invoke(Method.java:606)[:1.7.0_75]
	at org.apache.felix.scr.impl.helper.BaseMethod.invokeMethod(BaseMethod.java:231)
	at org.apache.felix.scr.impl.helper.BaseMethod.access$500(BaseMethod.java:39)
	at org.apache.felix.scr.impl.helper.BaseMethod$Resolved.invoke(BaseMethod.java:624)
	at org.apache.felix.scr.impl.helper.BaseMethod.invoke(BaseMethod.java:508)
	at org.apache.felix.scr.impl.helper.ActivateMethod.invoke(ActivateMethod.java:149)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:315)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:127)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:879)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:846)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:785)
	at org.apache.felix.framework.ServiceRegistrationImpl.getFactoryUnchecked(ServiceRegistrationImpl.java:345)
	at org.apache.felix.framework.ServiceRegistrationImpl.access$100(ServiceRegistrationImpl.java:47)
	at org.apache.felix.framework.ServiceRegistrationImpl$1.call(ServiceRegistrationImpl.java:249)
	at org.apache.felix.framework.Felix.runInContext(Felix.java:2188)
	at org.apache.felix.framework.ServiceRegistrationImpl.getService(ServiceRegistrationImpl.java:238)
	at org.apache.felix.framework.ServiceRegistry.getService(ServiceRegistry.java:328)
	at org.apache.felix.framework.Felix.getService(Felix.java:3819)
	at org.apache.felix.framework.BundleContextImpl.getService(BundleContextImpl.java:470)
	at org.apache.felix.scr.impl.helper.BindMethod.getServiceObject(BindMethod.java:572)
	at org.apache.felix.scr.impl.manager.DependencyManager.getServiceObject(DependencyManager.java:2006)
	at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.prebind(DependencyManager.java:1004)
	at org.apache.felix.scr.impl.manager.DependencyManager.prebind(DependencyManager.java:1433)
	at org.apache.felix.scr.impl.manager.AbstractComponentManager.collectDependencies(AbstractComponentManager.java:1143)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:815)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:785)
	at org.apache.felix.framework.ServiceRegistrationImpl.getFactoryUnchecked(ServiceRegistrationImpl.java:345)
	at org.apache.felix.framework.ServiceRegistrationImpl.access$100(ServiceRegistrationImpl.java:47)
	at org.apache.felix.framework.ServiceRegistrationImpl$1.call(ServiceRegistrationImpl.java:249)
	at org.apache.felix.framework.Felix.runInContext(Felix.java:2188)
	at org.apache.felix.framework.ServiceRegistrationImpl.getService(ServiceRegistrationImpl.java:238)
	at org.apache.felix.framework.ServiceRegistry.getService(ServiceRegistry.java:328)
	at org.apache.felix.framework.Felix.getService(Felix.java:3819)
	at org.apache.felix.framework.BundleContextImpl.getService(BundleContextImpl.java:470)
	at org.apache.aries.blueprint.container.AbstractServiceReferenceRecipe.getServiceSecurely(AbstractServiceReferenceRecipe.java:237)
	at org.apache.aries.blueprint.container.ReferenceRecipe.getService(ReferenceRecipe.java:241)
	at org.apache.aries.blueprint.container.ReferenceRecipe.access$000(ReferenceRecipe.java:55)
	at org.apache.aries.blueprint.container.ReferenceRecipe$ServiceDispatcher.call(ReferenceRecipe.java:294)
	at org.apache.aries.proxy.impl.ProxyHandler$1.invoke(ProxyHandler.java:54)
	at org.apache.aries.proxy.impl.ProxyHandler.invoke(ProxyHandler.java:119)
	at com.sun.proxy.$Proxy21.getContainers(Unknown Source)
	at io.fabric8.boot.commands.support.ContainerCompleter.complete(ContainerCompleter.java:33)
	at org.apache.karaf.shell.console.completer.ArgumentCompleter.verifyCompleter(ArgumentCompleter.java:347)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at org.apache.karaf.shell.console.completer.ArgumentCompleter.complete(ArgumentCompleter.java:301)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at org.apache.karaf.shell.console.completer.AggregateCompleter$Completion.complete(AggregateCompleter.java:86)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at org.apache.karaf.shell.console.completer.AggregateCompleter.complete(AggregateCompleter.java:51)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at org.apache.karaf.shell.console.completer.CommandsCompleter.complete(CommandsCompleter.java:76)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at org.apache.karaf.shell.console.jline.CompleterAsCompletor.complete(CompleterAsCompletor.java:32)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at jline.console.ConsoleReader.complete(ConsoleReader.java:3261)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at jline.console.ConsoleReader.readLine(ConsoleReader.java:2621)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at jline.console.ConsoleReader.readLine(ConsoleReader.java:2269)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at org.apache.karaf.shell.console.jline.Console.readAndParseCommand(Console.java:256)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at org.apache.karaf.shell.console.jline.Console.run(Console.java:185)[17:org.apache.karaf.shell.console:2.3.0.redhat-611429]
	at java.lang.Thread.run(Thread.java:745)[:1.7.0_75]
	at org.apache.karaf.shell.ssh.ShellFactoryImpl$ShellImpl$4.doRun(ShellFactoryImpl.java:158)[49:org.apache.karaf.shell.ssh:2.3.0.redhat-611429]
	at org.apache.karaf.shell.ssh.ShellFactoryImpl$ShellImpl$4$1.run(ShellFactoryImpl.java:149)
	at java.security.AccessController.doPrivileged(Native Method)[:1.7.0_75]
	at org.apache.karaf.jaas.modules.JaasHelper.doAs(JaasHelper.java:47)[27:org.apache.karaf.jaas.modules:2.3.0.redhat-611424]
	at org.apache.karaf.shell.ssh.ShellFactoryImpl$ShellImpl$4.run(ShellFactoryImpl.java:147)[49:org.apache.karaf.shell.ssh:2.3.0.redhat-611429]
Caused by: org.eclipse.jgit.api.errors.JGitInternalException: Stashing local changes did not successfully complete
	at org.eclipse.jgit.api.StashCreateCommand.call(StashCreateCommand.java:335)
	at io.fabric8.git.internal.GitDataStore.gitOperation(GitDataStore.java:927)
	at io.fabric8.git.internal.GitDataStore.gitOperation(GitDataStore.java:901)
	at io.fabric8.git.internal.GitDataStore.gitOperation(GitDataStore.java:896)
	at io.fabric8.git.internal.GitDataStore.forceGetVersions(GitDataStore.java:388)
	at io.fabric8.git.internal.GitDataStore.activateInternal(GitDataStore.java:180)
	... 63 more
Caused by: java.io.EOFException: Short read of block.
	at org.eclipse.jgit.util.IO.readFully(IO.java:248)
	at org.eclipse.jgit.dircache.DirCache.readFrom(DirCache.java:456)
	at org.eclipse.jgit.dircache.DirCache.read(DirCache.java:411)
	at org.eclipse.jgit.dircache.DirCache.lock(DirCache.java:227)
	at org.eclipse.jgit.dircache.DirCache.lock(DirCache.java:301)
	at org.eclipse.jgit.dircache.DirCache.lock(DirCache.java:267)
	at org.eclipse.jgit.lib.Repository.lockDirCache(Repository.java:1049)
	at org.eclipse.jgit.api.StashCreateCommand.call(StashCreateCommand.java:225)
	... 68 more