Full thread dump Java HotSpot(TM) Client VM (1.4.2_03-b02 mixed mode):

"System Bundle Shutdown" prio=1 tid=0x087f5a28 nid=0x3b0c in Object.wait() [5aede000..5aede854]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x463f2a18> (a java.lang.Thread)
        at java.lang.Thread.join(Thread.java:1001)
        - locked <0x463f2a18> (a java.lang.Thread)
        at java.lang.Thread.join(Thread.java:1054)
        at org.eclipse.jdt.internal.core.search.processing.JobManager.shutdown(JobManager.java:416)
        at org.eclipse.jdt.internal.core.JavaModelManager.shutdown(JavaModelManager.java:1833)
        at org.eclipse.jdt.core.JavaCore.stop(JavaCore.java:3601)
        at org.eclipse.osgi.framework.internal.core.BundleContextImpl$2.run(BundleContextImpl.java:994)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.eclipse.osgi.framework.internal.core.BundleContextImpl.stop(BundleContextImpl.java:990)
        at org.eclipse.osgi.framework.internal.core.BundleHost.stopWorker(BundleHost.java:502)
        at org.eclipse.osgi.framework.internal.core.AbstractBundle.stop(AbstractBundle.java:437)
        at org.eclipse.core.runtime.adaptor.BundleStopper.basicStopBundles(BundleStopper.java:75)
        at org.eclipse.core.runtime.adaptor.BundleStopper.stopBundles(BundleStopper.java:62)
        at org.eclipse.core.runtime.adaptor.EclipseAdaptor.frameworkStopping(EclipseAdaptor.java:551)
        at org.eclipse.osgi.framework.internal.core.Framework.shutdown(Framework.java:457)
        - locked <0x45b0aed8> (a org.eclipse.osgi.framework.internal.core.Framework)
        at org.eclipse.osgi.framework.internal.core.SystemBundle$1.run(SystemBundle.java:182)
        at java.lang.Thread.run(Thread.java:534)

"Worker-43" prio=1 tid=0x08c25c90 nid=0x3b0c in Object.wait() [59efd000..59efd854]
        at java.lang.Object.wait(Native Method)
        at org.eclipse.core.internal.jobs.WorkerPool.sleep(WorkerPool.java:166)
        - locked <0x45f11ba0> (a org.eclipse.core.internal.jobs.WorkerPool)
        at org.eclipse.core.internal.jobs.WorkerPool.startJob(WorkerPool.java:193)
        at org.eclipse.core.internal.jobs.Worker.run(Worker.java:59)

"Java indexing" daemon prio=1 tid=0x08938588 nid=0x3b0c in Object.wait() [5a711000..5a711854]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x463f2a60> (a org.eclipse.jdt.internal.core.search.indexing.IndexManager)
        at java.lang.Object.wait(Object.java:429)
        at org.eclipse.jdt.internal.core.search.processing.JobManager.run(JobManager.java:338)
        - locked <0x463f2a60> (a org.eclipse.jdt.internal.core.search.indexing.IndexManager)
        at java.lang.Thread.run(Thread.java:534)

"Reference Cleaner - 2" prio=1 tid=0x083916e8 nid=0x3b0c in Object.wait() [59e3c000..59e3c854]
        at java.lang.Object.wait(Native Method)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:111)
        - locked <0x45f69520> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:127)
        at org.eclipse.jface.action.ActionContributionItem$ImageCache$ReferenceCleanerThread.run(ActionContributionItem.java:207)

"Reference Cleaner - 1" prio=1 tid=0x08391440 nid=0x3b0c in Object.wait() [5916a000..5916a854]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x45f69590> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:111)
        - locked <0x45f69590> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:127)
        at org.eclipse.jface.action.ActionContributionItem$ImageCache$ReferenceCleanerThread.run(ActionContributionItem.java:207)

"Start Level Event Dispatcher" daemon prio=1 tid=0x08260200 nid=0x3b0c in Object.wait() [590d5000..590d5854]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x45b1a0f0> (a org.eclipse.osgi.framework.eventmgr.EventThread)
        at java.lang.Object.wait(Object.java:429)
        at org.eclipse.osgi.framework.eventmgr.EventThread.getNextEvent(EventThread.java:162)
        - locked <0x45b1a0f0> (a org.eclipse.osgi.framework.eventmgr.EventThread)
        at org.eclipse.osgi.framework.eventmgr.EventThread.run(EventThread.java:100)

"Framework Event Dispatcher" daemon prio=1 tid=0x08258490 nid=0x3b0c in Object.wait() [59054000..59054854]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x45b1a2b8> (a org.eclipse.osgi.framework.eventmgr.EventThread)
        at java.lang.Object.wait(Object.java:429)
        at org.eclipse.osgi.framework.eventmgr.EventThread.getNextEvent(EventThread.java:162)
        - locked <0x45b1a2b8> (a org.eclipse.osgi.framework.eventmgr.EventThread)
        at org.eclipse.osgi.framework.eventmgr.EventThread.run(EventThread.java:100)

"Signal Dispatcher" daemon prio=1 tid=0x0809d6f0 nid=0x3b0c waiting on condition [0..0]

"Finalizer" daemon prio=1 tid=0x080888b0 nid=0x3b0c in Object.wait() [589da000..589da854]
        at java.lang.Object.wait(Native Method)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:111)
        - locked <0x45af9188> (a java.lang.ref.ReferenceQueue$Lock)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:127)
        at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Reference Handler" daemon prio=1 tid=0x08087cc0 nid=0x3b0c in Object.wait() [58959000..58959854]
        at java.lang.Object.wait(Native Method)
        at java.lang.Object.wait(Object.java:429)
        at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:115)
        - locked <0x45af91f0> (a java.lang.ref.Reference$Lock)

"main" prio=1 tid=0x080524c8 nid=0x3b0c in Object.wait() [bfffc000..bfffca48]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x447f6420> (a org.eclipse.core.runtime.adaptor.Semaphore)
        at java.lang.Object.wait(Object.java:429)
        at org.eclipse.core.runtime.adaptor.Semaphore.acquire(Semaphore.java:33)
        - locked <0x447f6420> (a org.eclipse.core.runtime.adaptor.Semaphore)
        at org.eclipse.core.runtime.adaptor.EclipseStarter.stopSystemBundle(EclipseStarter.java:920)
        at org.eclipse.core.runtime.adaptor.EclipseStarter.shutdown(EclipseStarter.java:296)
        at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:144)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:324)
        at org.eclipse.core.launcher.Main.basicRun(Main.java:183)
        at org.eclipse.core.launcher.Main.run(Main.java:644)
        at org.eclipse.core.launcher.Main.main(Main.java:628)

"VM Thread" prio=1 tid=0x08086990 nid=0x3b0c runnable 

"VM Periodic Task Thread" prio=1 tid=0x0809ff00 nid=0x3b0c waiting on condition 
"Suspend Checker Thread" prio=1 tid=0x0809cd50 nid=0x3b0c runnable