If the initialization thread is interrupted by contextDestroyed, make that clear.

Otherwise get a meaningless error:
java.lang.InterruptedException
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:502)
    at org.jvnet.hudson.reactor.Reactor.execute(Reactor.java:267)
    at jenkins.InitReactorRunner.run(InitReactorRunner.java:44)
    at jenkins.model.Jenkins.executeReactor(Jenkins.java:915)
    at jenkins.model.Jenkins.<init>(Jenkins.java:814)
    at hudson.model.Hudson.<init>(Hudson.java:83)
    at hudson.model.Hudson.<init>(Hudson.java:79)
    at hudson.WebAppMain$3.run(WebAppMain.java:225)

core/src/main/java/hudson/WebAppMain.java

@@ -396,8 +396,10 @@ public class WebAppMain implements ServletContextListener {
         if(instance!=null)
             instance.cleanUp();
         Thread t = initThread;
-        if (t!=null)
+        if (t != null && t.isAlive()) {
+            LOGGER.log(Level.INFO, "Shutting down a Jenkins instance that was still starting up", new Throwable("reason"));
             t.interrupt();
+        }
 
         // Logger is in the system classloader, so if we don't do this
         // the whole web app will never be undepoyed.