Download part of the messages.log given in the URL. (I gave up after 55Mb.) Most of it consists of warnings led with

WARNING [glassfish-javaee]
org.netbeans.modules.j2ee.deployment.plugins.api.InstanceCreationException: No handlers for [C:\Program Files\glassfish-3.1.2\glassfish;C:\Program Files\glassfish-3.1.2\glassfish\domains\domain1]deployer:gfv3ee6wc:localhost:4848

which are derivative of the first warning

INFO [org.netbeans.core.startup.layers.BinaryFS]: value = org.netbeans.modules.glassfish.javaee.Hk2DeploymentFactory.createEe6 from J2EE/DeploymentPlugins/gfv3ee6/Factory.instance
java.lang.StackOverflowError

and containing a long recursion with the following cycle:

...
org.netbeans.modules.glassfish.javaee.Hk2DeploymentFactory.createEe6(Hk2DeploymentFactory.java:101)
sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:601)
org.netbeans.core.startup.layers.BinaryFS$AttrImpl$MethodAndParams.invoke(BinaryFS.java:746)
org.netbeans.core.startup.layers.BinaryFS$AttrImpl.getValue(BinaryFS.java:676)
org.netbeans.core.startup.layers.BinaryFS$BFSBase.getAttribute(BinaryFS.java:522)
org.openide.filesystems.MultiFileObject.getAttribute(MultiFileObject.java:930)
org.openide.filesystems.MultiFileObject.getAttribute(MultiFileObject.java:863)
org.openide.filesystems.MultiFileObject.getAttribute(MultiFileObject.java:926)
org.openide.filesystems.MultiFileObject.getAttribute(MultiFileObject.java:863)
org.openide.filesystems.MultiFileObject.getAttribute(MultiFileObject.java:791)
org.netbeans.core.startup.layers.BinaryFS$FileMap.get(BinaryFS.java:1101)
org.netbeans.modules.j2ee.deployment.plugins.spi.support.ProxyDeploymentFactory.getDelegate(ProxyDeploymentFactory.java:126)
org.netbeans.modules.j2ee.deployment.plugins.spi.support.ProxyDeploymentFactory.handlesURI(ProxyDeploymentFactory.java:96)
org.netbeans.modules.j2ee.deployment.impl.Server.handlesUri(Server.java:182)
org.netbeans.modules.j2ee.deployment.impl.ServerRegistry.addInstanceImpl(ServerRegistry.java:470)
org.netbeans.modules.j2ee.deployment.impl.ServerRegistry.addInstance(ServerRegistry.java:383)
org.netbeans.modules.j2ee.deployment.plugins.api.InstanceProperties.createInstancePropertiesNonPersistent(InstanceProperties.java:296)
org.netbeans.modules.glassfish.javaee.JavaEEServerModuleFactory.createModule(JavaEEServerModuleFactory.java:123)
org.netbeans.modules.glassfish.common.GlassfishInstance.updateFactories(GlassfishInstance.java:201)
org.netbeans.modules.glassfish.common.GlassfishInstance.updateModuleSupport(GlassfishInstance.java:223)
org.netbeans.modules.glassfish.common.GlassfishInstanceProvider.loadServerInstances(GlassfishInstanceProvider.java:502)
org.netbeans.modules.glassfish.common.GlassfishInstanceProvider.init(GlassfishInstanceProvider.java:438)
org.netbeans.modules.glassfish.common.GlassfishInstanceProvider.getEe6(GlassfishInstanceProvider.java:134)
org.netbeans.modules.glassfish.spi.ServerUtilities.getEe6Utilities(ServerUtilities.java:99)
org.netbeans.modules.glassfish.javaee.Hk2DeploymentFactory.createEe6(Hk2DeploymentFactory.java:101)
...