Recent changes on the affected server:
Jenkins-Update to 2.102, including all installed plugins
Update for WIndows 2012 R2

Jenkins refuses to start due to a thread deadlock during the startup process. This deadlock also affects HTTP request workers; so the server does not respond to HTTP requests anymore.

The stacks below show the deadlock between thread pool-6-thread-16 (a.k.a. GitSCM.onLoaded) and pool-6-thread-11. The last stack shows how RequestHandlerThread1 is blocked by the lock owned by GitSCM.onLoaded.

------------------------------------------------------------------------------
pool-6-thread-16

Name: GitSCM.onLoaded
State: WAITING on java.util.concurrent.locks.ReentrantLock$NonfairSync@29986f0 owned by: PreventRefreshFilter.initAutoRefreshFilter
Total blocked: 91 Total waited: 39

Stack trace:
sun.misc.Unsafe.park(Native Method)
java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:836)
java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireQueued(AbstractQueuedSynchronizer.java:870)
java.util.concurrent.locks.AbstractQueuedSynchronizer.acquire(AbstractQueuedSynchronizer.java:1199)
java.util.concurrent.locks.ReentrantLock$NonfairSync.lock(ReentrantLock.java:209)
java.util.concurrent.locks.ReentrantLock.lock(ReentrantLock.java:285)
com.google.inject.internal.CycleDetectingLock$CycleDetectingLockFactory$ReentrantCycleDetectingLock.lockOrDetectPotentialLocksCycle(CycleDetectingLock.java:160)
com.google.inject.internal.SingletonScope$1.get(SingletonScope.java:136)
hudson.ExtensionFinder$GuiceFinder$FaultTolerantScope$1.get(ExtensionFinder.java:424)
com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:41)
com.google.inject.internal.InjectorImpl$2$1.call(InjectorImpl.java:1016)
com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1092)
com.google.inject.internal.InjectorImpl$2.get(InjectorImpl.java:1012)
hudson.ExtensionFinder$GuiceFinder._find(ExtensionFinder.java:386)
hudson.ExtensionFinder$GuiceFinder.find(ExtensionFinder.java:377)
hudson.ClassicPluginStrategy.findComponents(ClassicPluginStrategy.java:482)
hudson.ExtensionList.load(ExtensionList.java:366)
hudson.ExtensionList.ensureLoaded(ExtensionList.java:304)

• locked hudson.ExtensionList$Lock@5cfdc450
  hudson.ExtensionList.iterator(ExtensionList.java:158)
  jenkins.model.Jenkins.getDescriptorByType(Jenkins.java:1519)
  hudson.plugins.git.GitSCM.onLoaded(GitSCM.java:1859)
  sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
  sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  java.lang.reflect.Method.invoke(Method.java:498)
  hudson.init.TaskMethodFinder.invoke(TaskMethodFinder.java:104)
  hudson.init.TaskMethodFinder$TaskImpl.run(TaskMethodFinder.java:175)
  org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:282)
  jenkins.model.Jenkins$5.runTask(Jenkins.java:1063)
  org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:210)
  org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:117)
  java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
  java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
  java.lang.Thread.run(Thread.java:748)

------------------------------------------------------------------------------
pool-6-thread-11

Name: PreventRefreshFilter.initAutoRefreshFilter
State: BLOCKED on hudson.ExtensionList$Lock@5cfdc450 owned by: GitSCM.onLoaded
Total blocked: 10 Total waited: 41

Stack trace:
hudson.ExtensionList.ensureLoaded(ExtensionList.java:303)
hudson.ExtensionList.iterator(ExtensionList.java:158)
hudson.ExtensionList.get(ExtensionList.java:149)
org.jenkinsci.plugins.scriptsecurity.scripts.ScriptApproval.get(ScriptApproval.java:97)
org.jenkinsci.plugins.scriptsecurity.sandbox.groovy.SecureGroovyScript.configuring(SecureGroovyScript.java:126)
org.jenkinsci.plugins.scriptsecurity.sandbox.groovy.SecureGroovyScript.readResolve(SecureGroovyScript.java:102)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
com.thoughtworks.xstream.converters.reflection.SerializationMethodInvoker.callReadResolve(SerializationMethodInvoker.java:66)
hudson.util.RobustReflectionConverter.unmarshal(RobustReflectionConverter.java:271)
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
hudson.util.RobustReflectionConverter.unmarshalField(RobustReflectionConverter.java:393)
hudson.util.RobustReflectionConverter.doUnmarshal(RobustReflectionConverter.java:331)
hudson.util.RobustReflectionConverter.unmarshal(RobustReflectionConverter.java:270)
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:50)
com.thoughtworks.xstream.core.TreeUnmarshaller.start(TreeUnmarshaller.java:134)
com.thoughtworks.xstream.core.AbstractTreeMarshallingStrategy.unmarshal(AbstractTreeMarshallingStrategy.java:32)
com.thoughtworks.xstream.XStream.unmarshal(XStream.java:1189)
hudson.util.XStream2.unmarshal(XStream2.java:147)
hudson.util.XStream2.unmarshal(XStream2.java:118)
com.thoughtworks.xstream.XStream.unmarshal(XStream.java:1173)
hudson.XmlFile.unmarshal(XmlFile.java:179)
hudson.XmlFile.unmarshal(XmlFile.java:162)
hudson.model.Descriptor.load(Descriptor.java:893)

• locked hudson.plugins.claim.ClaimConfig@1d46c412
  hudson.plugins.claim.ClaimConfig.<init>(ClaimConfig.java:24)
  hudson.plugins.claim.ClaimConfig$$FastClassByGuice$$74f9760b.newInstance(<generated>)
  com.google.inject.internal.cglib.reflect.$FastConstructor.newInstance(FastConstructor.java:40)
  com.google.inject.internal.DefaultConstructionProxyFactory$1.newInstance(DefaultConstructionProxyFactory.java:61)
  com.google.inject.internal.ConstructorInjector.provision(ConstructorInjector.java:105)
  com.google.inject.internal.ConstructorInjector.construct(ConstructorInjector.java:85)
  com.google.inject.internal.ConstructorBindingImpl$Factory.get(ConstructorBindingImpl.java:267)
  com.google.inject.internal.ProviderToInternalFactoryAdapter$1.call(ProviderToInternalFactoryAdapter.java:46)
  com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1103)
  com.google.inject.internal.ProviderToInternalFactoryAdapter.get(ProviderToInternalFactoryAdapter.java:40)
  com.google.inject.internal.SingletonScope$1.get(SingletonScope.java:145)
  hudson.ExtensionFinder$GuiceFinder$FaultTolerantScope$1.get(ExtensionFinder.java:424)
  com.google.inject.internal.InternalFactoryToProviderAdapter.get(InternalFactoryToProviderAdapter.java:41)
  com.google.inject.internal.InjectorImpl$2$1.call(InjectorImpl.java:1016)
  com.google.inject.internal.InjectorImpl.callInContext(InjectorImpl.java:1092)
  com.google.inject.internal.InjectorImpl$2.get(InjectorImpl.java:1012)
  com.google.inject.internal.InjectorImpl.getInstance(InjectorImpl.java:1051)
  jenkins.ProxyInjector.getInstance(ProxyInjector.java:98)
  hudson.init.TaskMethodFinder.lookUp(TaskMethodFinder.java:124)
  hudson.init.TaskMethodFinder.invoke(TaskMethodFinder.java:102)
  hudson.init.TaskMethodFinder$TaskImpl.run(TaskMethodFinder.java:175)
  org.jvnet.hudson.reactor.Reactor.runTask(Reactor.java:282)
  jenkins.model.Jenkins$5.runTask(Jenkins.java:1063)
  org.jvnet.hudson.reactor.Reactor$2.run(Reactor.java:210)
  org.jvnet.hudson.reactor.Reactor$Node.run(Reactor.java:117)
  java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
  java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
  java.lang.Thread.run(Thread.java:748)

------------------------------------------------------------------------------
RequestHandlerThread1

Name: Handling GET / from 10.10.15.31 : RequestHandlerThread1 HudsonIsLoading/index.jelly
State: BLOCKED on hudson.ExtensionList$Lock@5cfdc450 owned by: GitSCM.onLoaded
Total blocked: 1 Total waited: 0

Stack trace:
hudson.ExtensionList.ensureLoaded(ExtensionList.java:303)
hudson.ExtensionList.iterator(ExtensionList.java:158)
jenkins.JenkinsHttpSessionListener.sessionCreated(JenkinsHttpSessionListener.java:50)
org.eclipse.jetty.server.session.SessionHandler.newHttpSession(SessionHandler.java:810)
org.eclipse.jetty.server.Request.getSession(Request.java:1550)
org.eclipse.jetty.server.Request.getSession(Request.java:1523)
javax.servlet.http.HttpServletRequestWrapper.getSession(HttpServletRequestWrapper.java:279)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.apache.commons.jexl.util.introspection.UberspectImpl$VelMethodImpl.invoke(UberspectImpl.java:258)
org.apache.commons.jexl.parser.ASTMethod.execute(ASTMethod.java:104)
org.apache.commons.jexl.parser.ASTReference.execute(ASTReference.java:83)
org.apache.commons.jexl.parser.ASTReference.value(ASTReference.java:57)
org.apache.commons.jexl.parser.ASTReferenceExpression.value(ASTReferenceExpression.java:51)
org.apache.commons.jexl.ExpressionImpl.evaluate(ExpressionImpl.java:80)
hudson.ExpressionFactory2$JexlExpression.evaluate(ExpressionFactory2.java:74)
org.apache.commons.jelly.tags.core.CoreTagLibrary$3.run(CoreTagLibrary.java:134)
org.apache.commons.jelly.impl.ScriptBlock.run(ScriptBlock.java:95)
org.apache.commons.jelly.tags.core.CoreTagLibrary$2.run(CoreTagLibrary.java:105)
org.kohsuke.stapler.jelly.CallTagLibScript.run(CallTagLibScript.java:120)
org.apache.commons.jelly.impl.ScriptBlock.run(ScriptBlock.java:95)
org.apache.commons.jelly.tags.core.CoreTagLibrary$2.run(CoreTagLibrary.java:105)
org.kohsuke.stapler.jelly.JellyViewScript.run(JellyViewScript.java:95)
org.kohsuke.stapler.jelly.DefaultScriptInvoker.invokeScript(DefaultScriptInvoker.java:63)
org.kohsuke.stapler.jelly.DefaultScriptInvoker.invokeScript(DefaultScriptInvoker.java:53)
org.kohsuke.stapler.jelly.JellyClassTearOff.serveIndexJelly(JellyClassTearOff.java:112)
org.kohsuke.stapler.jelly.JellyFacet.handleIndexRequest(JellyFacet.java:140)
org.kohsuke.stapler.IndexViewDispatcher.dispatch(IndexViewDispatcher.java:30)
org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:715)
org.kohsuke.stapler.Stapler.invoke(Stapler.java:845)
org.kohsuke.stapler.Stapler.invoke(Stapler.java:649)
org.kohsuke.stapler.Stapler.service(Stapler.java:238)
javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:841)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1650)
hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:154)
com.smartcodeltd.jenkinsci.plugin.assetbundler.filters.LessCSS.doFilter(LessCSS.java:47)
hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:151)
hudson.plugins.greenballs.GreenBallFilter.doFilter(GreenBallFilter.java:59)
hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:151)
hudson.util.PluginServletFilter.doFilter(PluginServletFilter.java:157)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
hudson.security.csrf.CrumbFilter.doFilter(CrumbFilter.java:64)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
hudson.security.HudsonFilter.doFilter(HudsonFilter.java:169)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
org.kohsuke.stapler.compression.CompressionFilter.doFilter(CompressionFilter.java:49)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
hudson.util.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:82)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
org.kohsuke.stapler.DiagnosticThreadNameFilter.doFilter(DiagnosticThreadNameFilter.java:30)
org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637)
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533)
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:524)
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190)
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595)
org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188)
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253)
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168)
org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473)
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564)
org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166)
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155)
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
org.eclipse.jetty.server.Server.handle(Server.java:564)
org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:317)
org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:251)
org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279)
org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:110)
org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124)
org.eclipse.jetty.util.thread.Invocable.invokePreferred(Invocable.java:128)
org.eclipse.jetty.util.thread.Invocable$InvocableExecutor.invoke(Invocable.java:222)
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:294)
org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:126)
org.eclipse.jetty.io.ManagedSelector$$Lambda$16/549293029.run(Unknown Source)
winstone.BoundedExecutorService$1.run(BoundedExecutorService.java:77)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
java.lang.Thread.run(Thread.java:748)