diff --git a/platform/lang-impl/src/com/intellij/util/fileIndex/AbstractFileIndex.java b/platform/lang-impl/src/com/intellij/util/fileIndex/AbstractFileIndex.java
index 0993ac7c31c8..81ca7db33dc3 100644
--- a/platform/lang-impl/src/com/intellij/util/fileIndex/AbstractFileIndex.java
+++ b/platform/lang-impl/src/com/intellij/util/fileIndex/AbstractFileIndex.java
@@ -334,7 +334,7 @@ public abstract class AbstractFileIndex<IndexEntry extends FileIndexEntry> imple
       myFileTypesToRefresh = fileTypesToRefresh;
     }
 
-    public VirtualFile[] queryNeededFiles() {
+    public VirtualFile[] queryNeededFiles(ProgressIndicator indicator) {
       return AbstractFileIndex.this.queryNeededFiles(myIncludeChangedFiles, myFileTypesToRefresh);
     }
 
diff --git a/platform/lang-impl/src/com/intellij/util/fileIndex/FileIndexRefreshCacheUpdater.java b/platform/lang-impl/src/com/intellij/util/fileIndex/FileIndexRefreshCacheUpdater.java
index 17bec369758a..681ad1e118c3 100644
--- a/platform/lang-impl/src/com/intellij/util/fileIndex/FileIndexRefreshCacheUpdater.java
+++ b/platform/lang-impl/src/com/intellij/util/fileIndex/FileIndexRefreshCacheUpdater.java
@@ -19,6 +19,7 @@ package com.intellij.util.fileIndex;
 import com.intellij.ide.caches.CacheUpdater;
 import com.intellij.ide.caches.FileContent;
 import com.intellij.openapi.Disposable;
+import com.intellij.openapi.progress.ProgressIndicator;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.roots.ex.ProjectRootManagerEx;
 import com.intellij.openapi.vfs.*;
@@ -70,7 +71,7 @@ public class FileIndexRefreshCacheUpdater extends VirtualFileAdapter implements
     return 0;
   }
 
-  public VirtualFile[] queryNeededFiles() {
+  public VirtualFile[] queryNeededFiles(ProgressIndicator indicator) {
     return VfsUtil.toVirtualFileArray(myChangedFiles);
   }
 
diff --git a/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndex.java b/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndex.java
index cdad30482b05..ced6e0cc5290 100644
--- a/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndex.java
+++ b/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndex.java
@@ -1937,7 +1937,7 @@ public class FileBasedIndex implements ApplicationComponent {
     }
   }
 
-  public static void iterateIndexableFiles(final ContentIterator processor, Project project) {
+  public static void iterateIndexableFiles(final ContentIterator processor, Project project, ProgressIndicator indicator) {
     if (project.isDisposed()) {
       return;
     }
@@ -1948,7 +1948,6 @@ public class FileBasedIndex implements ApplicationComponent {
     if (project.isDisposed()) {
       return;
     }
-    ProgressIndicator indicator = ProgressManager.getInstance().getProgressIndicator();
 
     Set<VirtualFile> visitedRoots = new HashSet<VirtualFile>();
     for (IndexedRootsProvider provider : Extensions.getExtensions(IndexedRootsProvider.EP_NAME)) {
@@ -1999,6 +1998,7 @@ public class FileBasedIndex implements ApplicationComponent {
   private static void iterateRecursively(@Nullable final VirtualFile root, final ContentIterator processor, ProgressIndicator indicator) {
     if (root != null) {
       if (indicator != null) {
+        indicator.checkCanceled();
         indicator.setText2(root.getPresentableUrl());
       }
 
@@ -2011,7 +2011,8 @@ public class FileBasedIndex implements ApplicationComponent {
             processor.processFile(file);
           }
         }
-      } else {
+      }
+      else {
         processor.processFile(root);
       }
     }
diff --git a/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexProjectHandler.java b/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexProjectHandler.java
index c402b80d3050..2859e104bbcc 100644
--- a/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexProjectHandler.java
+++ b/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndexProjectHandler.java
@@ -25,6 +25,7 @@ import com.intellij.ide.startup.StartupManagerEx;
 import com.intellij.openapi.components.AbstractProjectComponent;
 import com.intellij.openapi.file.exclude.ProjectFileExclusionManager;
 import com.intellij.openapi.fileTypes.FileTypeManager;
+import com.intellij.openapi.progress.ProgressIndicator;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.project.ProjectManager;
 import com.intellij.openapi.project.ProjectManagerAdapter;
@@ -105,7 +106,7 @@ public class FileBasedIndexProjectHandler extends AbstractProjectComponent imple
       return myIndex.getNumberOfPendingInvalidations();
     }
 
-    public VirtualFile[] queryNeededFiles() {
+    public VirtualFile[] queryNeededFiles(ProgressIndicator indicator) {
       Collection<VirtualFile> files = myIndex.getFilesToUpdate(myProject);
       return VfsUtil.toVirtualFileArray(files);
     }
diff --git a/platform/lang-impl/src/com/intellij/util/indexing/UnindexedFilesUpdater.java b/platform/lang-impl/src/com/intellij/util/indexing/UnindexedFilesUpdater.java
index 0f5577238ff7..dc9179058f66 100644
--- a/platform/lang-impl/src/com/intellij/util/indexing/UnindexedFilesUpdater.java
+++ b/platform/lang-impl/src/com/intellij/util/indexing/UnindexedFilesUpdater.java
@@ -19,6 +19,7 @@ package com.intellij.util.indexing;
 import com.intellij.ide.caches.CacheUpdater;
 import com.intellij.ide.caches.FileContent;
 import com.intellij.openapi.diagnostic.Logger;
+import com.intellij.openapi.progress.ProgressIndicator;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.roots.CollectingContentIterator;
 import com.intellij.openapi.vfs.VfsUtil;
@@ -45,10 +46,10 @@ public class UnindexedFilesUpdater implements CacheUpdater {
     return myIndex.getNumberOfPendingInvalidations();
   }
 
-  public VirtualFile[] queryNeededFiles() {
+  public VirtualFile[] queryNeededFiles(ProgressIndicator indicator) {
     CollectingContentIterator finder = myIndex.createContentIterator();
     long l = System.currentTimeMillis();
-    FileBasedIndex.iterateIndexableFiles(finder, myProject);
+    FileBasedIndex.iterateIndexableFiles(finder, myProject, indicator);
     LOG.info("Indexable files iterated in " + (System.currentTimeMillis() - l) + " ms");
     List<VirtualFile> files = finder.getFiles();
     LOG.info("Unindexed files update started: " + files.size() + " files to update");
diff --git a/platform/platform-api/src/com/intellij/ide/caches/CacheUpdater.java b/platform/platform-api/src/com/intellij/ide/caches/CacheUpdater.java
index 68cece670ad2..219f23bced4f 100644
--- a/platform/platform-api/src/com/intellij/ide/caches/CacheUpdater.java
+++ b/platform/platform-api/src/com/intellij/ide/caches/CacheUpdater.java
@@ -16,12 +16,13 @@
 
 package com.intellij.ide.caches;
 
+import com.intellij.openapi.progress.ProgressIndicator;
 import com.intellij.openapi.vfs.VirtualFile;
 
 public interface CacheUpdater {
   int getNumberOfPendingUpdateJobs();
 
-  VirtualFile[] queryNeededFiles();
+  VirtualFile[] queryNeededFiles(ProgressIndicator indicator);
 
   void processFile(FileContent fileContent);
 
diff --git a/platform/platform-impl/src/com/intellij/internal/ToggleDumbModeAction.java b/platform/platform-impl/src/com/intellij/internal/ToggleDumbModeAction.java
index 51c59a3eb1cc..92e4002c5578 100644
--- a/platform/platform-impl/src/com/intellij/internal/ToggleDumbModeAction.java
+++ b/platform/platform-impl/src/com/intellij/internal/ToggleDumbModeAction.java
@@ -21,6 +21,7 @@ import com.intellij.openapi.actionSystem.AnAction;
 import com.intellij.openapi.actionSystem.AnActionEvent;
 import com.intellij.openapi.actionSystem.PlatformDataKeys;
 import com.intellij.openapi.actionSystem.Presentation;
+import com.intellij.openapi.progress.ProgressIndicator;
 import com.intellij.openapi.project.DumbAware;
 import com.intellij.openapi.project.DumbServiceImpl;
 import com.intellij.openapi.project.Project;
@@ -48,7 +49,7 @@ public class ToggleDumbModeAction extends AnAction implements DumbAware {
           return 0;
         }
 
-        public VirtualFile[] queryNeededFiles() {
+        public VirtualFile[] queryNeededFiles(ProgressIndicator indicator) {
           while (myDumb) {
             try {
               Thread.sleep(100);
diff --git a/platform/platform-impl/src/com/intellij/openapi/application/impl/ApplicationImpl.java b/platform/platform-impl/src/com/intellij/openapi/application/impl/ApplicationImpl.java
index ddcdc4150324..cd634ec99ef5 100644
--- a/platform/platform-impl/src/com/intellij/openapi/application/impl/ApplicationImpl.java
+++ b/platform/platform-impl/src/com/intellij/openapi/application/impl/ApplicationImpl.java
@@ -544,6 +544,9 @@ public class ApplicationImpl extends ComponentManagerImpl implements Application
 
   public void dispose() {
     fireApplicationExiting();
+
+    ShutDownTracker.getInstance().ensureStopperThreadsFinished();
+
     disposeComponents();
 
     ourThreadExecutorsService.shutdownNow();
diff --git a/platform/platform-impl/src/com/intellij/openapi/progress/impl/ProgressManagerImpl.java b/platform/platform-impl/src/com/intellij/openapi/progress/impl/ProgressManagerImpl.java
index 298403bc1585..3583bfe99be4 100644
--- a/platform/platform-impl/src/com/intellij/openapi/progress/impl/ProgressManagerImpl.java
+++ b/platform/platform-impl/src/com/intellij/openapi/progress/impl/ProgressManagerImpl.java
@@ -20,29 +20,22 @@ import com.intellij.openapi.application.Application;
 import com.intellij.openapi.application.ApplicationManager;
 import com.intellij.openapi.application.ModalityState;
 import com.intellij.openapi.application.ex.ApplicationEx;
-import com.intellij.openapi.application.ex.ApplicationManagerEx;
 import com.intellij.openapi.progress.*;
 import com.intellij.openapi.progress.util.ProgressWindow;
 import com.intellij.openapi.progress.util.SmoothProgressAdapter;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.util.Comparing;
 import com.intellij.openapi.util.Disposer;
-import com.intellij.openapi.util.Pair;
 import com.intellij.openapi.wm.WindowManager;
 import com.intellij.openapi.wm.ex.ProgressIndicatorEx;
 import com.intellij.psi.PsiLock;
 import com.intellij.ui.SystemNotifications;
-import com.intellij.util.containers.SortedList;
-import gnu.trove.THashMap;
 import org.jetbrains.annotations.*;
 
 import javax.swing.*;
 import java.awt.*;
 import java.lang.reflect.Field;
 import java.lang.reflect.Method;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
 import java.util.concurrent.atomic.AtomicInteger;
 
 public class ProgressManagerImpl extends ProgressManager implements Disposable{
@@ -57,7 +50,6 @@ public class ProgressManagerImpl extends ProgressManager implements Disposable{
   @NonNls private static final String NAME = "Progress Cancel Checker";
   private static final boolean DISABLED = Comparing.equal(System.getProperty(PROCESS_CANCELED_EXCEPTION), "disabled");
 
-  private static final Map<String, Long> myWastedTime = new THashMap<String, Long>();
   private volatile boolean enabled = true;
 
   public ProgressManagerImpl(Application application) {
@@ -274,7 +266,6 @@ public class ProgressManagerImpl extends ProgressManager implements Disposable{
     else {
       task.onCancel();
     }
-    moreTimeWasted(time, task);
     return result;
   }
 
@@ -362,7 +353,6 @@ public class ProgressManagerImpl extends ProgressManager implements Disposable{
           ApplicationManager.getApplication().invokeLater(new Runnable() {
             public void run() {
               task.onCancel();
-              moreTimeWasted(time, task);
             }
           }, ModalityState.NON_MODAL);
         }
@@ -377,7 +367,6 @@ public class ProgressManagerImpl extends ProgressManager implements Disposable{
           ApplicationManager.getApplication().invokeLater(new Runnable() {
             public void run() {
               task.onSuccess();
-              moreTimeWasted(time, task);
             }
           }, ModalityState.NON_MODAL);
         }
@@ -395,40 +384,6 @@ public class ProgressManagerImpl extends ProgressManager implements Disposable{
     }
   }
 
-  private static void moreTimeWasted(long time, Task timeEater) {
-    if (!ApplicationManagerEx.getApplicationEx().isInternal()) return;
-    
-    synchronized (myWastedTime) {
-      String title = timeEater.getTitle();
-      Long total = myWastedTime.get(title);
-      myWastedTime.put(title, total == null ? time : total + time);
-    }
-  }
-
-  public static long getWastedTime() {
-    synchronized (myWastedTime) {
-      long result = 0;
-      for (Map.Entry<String, Long> each : myWastedTime.entrySet()) {
-        result += each.getValue();
-      }
-      return result;
-    }
-  }
-
-  public static List<Pair<String, Long>> getTimeWasters() {
-    synchronized (myWastedTime) {
-      SortedList<Pair<String, Long>> result = new SortedList<Pair<String, Long>>(new Comparator<Pair<String, Long>>() {
-        public int compare(Pair<String, Long> o1, Pair<String, Long> o2) {
-          return o2.second.compareTo(o1.second);
-        }
-      });
-      for (Map.Entry<String, Long> each : myWastedTime.entrySet()) {
-        result.add(Pair.create(each.getKey(), each.getValue()));
-      }
-      return result;
-    }
-  }
-
   public void run(@NotNull final Task task) {
     if (task.isHeadless()) {
       new TaskRunnable(task, new EmptyProgressIndicator()).run();
diff --git a/platform/platform-impl/src/com/intellij/openapi/project/CacheUpdateSession.java b/platform/platform-impl/src/com/intellij/openapi/project/CacheUpdateSession.java
index 2dea17c17175..7b6f8ae021bd 100644
--- a/platform/platform-impl/src/com/intellij/openapi/project/CacheUpdateSession.java
+++ b/platform/platform-impl/src/com/intellij/openapi/project/CacheUpdateSession.java
@@ -48,7 +48,7 @@ public class CacheUpdateSession {
         indicator.checkCanceled();
         try {
           jobsCount += each.getNumberOfPendingUpdateJobs();
-          List<VirtualFile> updaterFiles = Arrays.asList(each.queryNeededFiles());
+          List<VirtualFile> updaterFiles = Arrays.asList(each.queryNeededFiles(indicator));
           processedUpdaters.add(each);
           myFilesToUpdate.addAll(updaterFiles);
           myUpdatersWithFiles.add(Pair.create(each, (Collection<VirtualFile>)new THashSet<VirtualFile>(updaterFiles)));
diff --git a/platform/platform-impl/src/com/intellij/openapi/project/DumbServiceImpl.java b/platform/platform-impl/src/com/intellij/openapi/project/DumbServiceImpl.java
index 857a5e094fdb..a474a9e0f242 100644
--- a/platform/platform-impl/src/com/intellij/openapi/project/DumbServiceImpl.java
+++ b/platform/platform-impl/src/com/intellij/openapi/project/DumbServiceImpl.java
@@ -26,6 +26,7 @@ import com.intellij.openapi.progress.util.ProgressIndicatorBase;
 import com.intellij.openapi.ui.MessageType;
 import com.intellij.openapi.ui.popup.BalloonHandler;
 import com.intellij.openapi.util.Ref;
+import com.intellij.openapi.util.ShutDownTracker;
 import com.intellij.openapi.wm.AppIconScheme;
 import com.intellij.openapi.wm.IdeFrame;
 import com.intellij.openapi.wm.WindowManager;
@@ -293,7 +294,7 @@ public class DumbServiceImpl extends DumbService {
 
               @Override
               public void finish(@NotNull TaskInfo task) {
-                UIUtil.invokeAndWaitIfNeeded(new Runnable() {
+                UIUtil.invokeLaterIfNeeded(new Runnable() {
                   public void run() {
                     AppIcon appIcon = AppIcon.getInstance();
                     if (appIcon.hideProgress("indexUpdate")) {
@@ -327,11 +328,15 @@ public class DumbServiceImpl extends DumbService {
               }
             });
 
+          final ShutDownTracker shutdownTracker = ShutDownTracker.getInstance();
+          final Thread self = Thread.currentThread();
           try {
             HeavyProcessLatch.INSTANCE.processStarted();
+            shutdownTracker.registerStopperThread(self);
             runAction(proxy, myAction);
           }
           finally {
+            shutdownTracker.unregisterStopperThread(self);
             HeavyProcessLatch.INSTANCE.processFinished();
           }
         }
diff --git a/platform/util/src/com/intellij/openapi/util/ShutDownTracker.java b/platform/util/src/com/intellij/openapi/util/ShutDownTracker.java
index 4958360f44ec..b4b50d0e4cf4 100644
--- a/platform/util/src/com/intellij/openapi/util/ShutDownTracker.java
+++ b/platform/util/src/com/intellij/openapi/util/ShutDownTracker.java
@@ -52,26 +52,8 @@ public class ShutDownTracker implements Runnable {
   public void run() {
     myIsShutdownHookRunning = true;
 
-    Thread[] threads = getStopperThreads();
-    while (threads.length > 0) {
-      Thread thread = threads[0];
-      if (!thread.isAlive()) {
-        if (isRegistered(thread)) {
-          LOG.error("Thread '" + thread.getName() + "' did not unregister itself from ShutDownTracker.");
-          unregisterStopperThread(thread);
-        }
-      }
-      else {
-        try {
-          thread.join(100);
-        }
-        catch (InterruptedException ignored) {
-        }
-      }
-      threads = getStopperThreads();
-    }
-    
-    
+    ensureStopperThreadsFinished();
+
     for (Runnable task = removeLast(myShutdownTasks); task != null; task = removeLast(myShutdownTasks)) {
       //  task can change myShutdownTasks
       try {
@@ -92,6 +74,27 @@ public class ShutDownTracker implements Runnable {
     }
   }
 
+  public final void ensureStopperThreadsFinished() {
+    Thread[] threads = getStopperThreads();
+    while (threads.length > 0) {
+      Thread thread = threads[0];
+      if (!thread.isAlive()) {
+        if (isRegistered(thread)) {
+          LOG.error("Thread '" + thread.getName() + "' did not unregister itself from ShutDownTracker.");
+          unregisterStopperThread(thread);
+        }
+      }
+      else {
+        try {
+          thread.join(100);
+        }
+        catch (InterruptedException ignored) {
+        }
+      }
+      threads = getStopperThreads();
+    }
+  }
+
   private synchronized boolean isRegistered(@NotNull Thread thread) {
     return myThreads.contains(thread);
   }