diff --git a/platform/lang-impl/src/com/intellij/psi/impl/source/PsiFileImpl.java b/platform/lang-impl/src/com/intellij/psi/impl/source/PsiFileImpl.java
index d6685573880f..595e8b09b3d3 100644
--- a/platform/lang-impl/src/com/intellij/psi/impl/source/PsiFileImpl.java
+++ b/platform/lang-impl/src/com/intellij/psi/impl/source/PsiFileImpl.java
@@ -60,6 +60,7 @@ import com.intellij.util.PatchedSoftReference;
 import com.intellij.util.PatchedWeakReference;
 import com.intellij.util.containers.ContainerUtil;
 import com.intellij.util.indexing.FileBasedIndex;
+import com.intellij.util.indexing.IndexingStamp;
 import com.intellij.util.text.CharArrayUtil;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -605,7 +606,8 @@ public abstract class PsiFileImpl extends ElementBase implements PsiFileEx, PsiF
     final IElementType contentElementType = getContentElementType();
     if (!(contentElementType instanceof IStubFileElementType)) {
       final FileViewProvider viewProvider = getViewProvider();
-      throw new AssertionError("A stub in a non-stub file '" + vFile +"'; isValid()=" + vFile.isValid() +
+      throw new AssertionError("A stub in a non-stub file '" + vFile +"'; isValid()=" + vFile.isValid() + 
+                               "; IndexStamp="+ IndexingStamp.getIndexStamp(vFile, StubUpdatingIndex.INDEX_ID) +
                                "; Type: " + contentElementType + "; " +
                                "Psi roots: " + viewProvider.getAllFiles() + "; " +
                                " StubUpdatingIndex.canHaveStub(vFile)=" + StubUpdatingIndex.canHaveStub(vFile) + 
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 7fe967d8856b..1b129166cf66 100644
--- a/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndex.java
+++ b/platform/lang-impl/src/com/intellij/util/indexing/FileBasedIndex.java
@@ -1573,16 +1573,12 @@ public class FileBasedIndex implements ApplicationComponent {
             ApplicationManager.getApplication().runReadAction(new Runnable() {
               public void run() {
                 for (ID<?, ?> indexId : affectedIndices) {
-                  IndexingStamp.update(file, indexId, -1L);
+                  IndexingStamp.update(file, indexId, -2L);
                 }
               }
             });
-            iterateIndexableFiles(file, new Processor<VirtualFile>() {
-              public boolean process(final VirtualFile file) {
-                scheduleForUpdate(file);
-                return true;
-              }
-            });
+            // the file is for sure not a dir and it was previously indexed by at least one index
+            scheduleForUpdate(file);
           }
           else {
             final InvalidationTask invalidator = new InvalidationTask(file) {
@@ -1631,7 +1627,9 @@ public class FileBasedIndex implements ApplicationComponent {
 
     public void ensureAllInvalidateTasksCompleted() {
       final int size = getNumberOfPendingInvalidations();
-      if (size == 0) return;
+      if (size == 0) {
+        return;
+      }
       final ProgressIndicator current = ProgressManager.getInstance().getProgressIndicator();
       final ProgressIndicator indicator = current != null ? current : new EmptyProgressIndicator();
       indicator.setText("");
diff --git a/platform/lang-impl/src/com/intellij/util/indexing/IndexingStamp.java b/platform/lang-impl/src/com/intellij/util/indexing/IndexingStamp.java
index 72eec3aacfe7..bf87bb3ea348 100644
--- a/platform/lang-impl/src/com/intellij/util/indexing/IndexingStamp.java
+++ b/platform/lang-impl/src/com/intellij/util/indexing/IndexingStamp.java
@@ -142,11 +142,7 @@ public class IndexingStamp {
 
   public static boolean isFileIndexed(VirtualFile file, ID<?, ?> indexName, final long indexCreationStamp) {
     try {
-      if (file instanceof NewVirtualFile && file.isValid()) {
-        synchronized (myTimestampsCache) {
-          return myTimestampsCache.get(file).get(indexName) == indexCreationStamp;
-        }
-      }
+      return getIndexStamp(file, indexName) == indexCreationStamp;
     }
     catch (RuntimeException e) {
       final Throwable cause = e.getCause();
@@ -158,6 +154,15 @@ public class IndexingStamp {
     return false;
   }
 
+  public static long getIndexStamp(VirtualFile file, ID<?, ?> indexName) {
+    if (file instanceof NewVirtualFile && file.isValid()) {
+      synchronized (myTimestampsCache) {
+        return myTimestampsCache.get(file).get(indexName);
+      }
+    }
+    return 0L;
+  }
+
   public static void update(final VirtualFile file, final ID<?, ?> indexName, final long indexCreationStamp) {
     try {
       if (file instanceof NewVirtualFile && file.isValid()) {