When the file content is the same as the being removed overlay contents, ignore the change.

pkg/analyzer/lib/src/generated/engine.dart

 // Copyright (c) 2014, the Dart project authors.  Please see the AUTHORS file
 // for details. All rights reserved. Use of this source code is governed by a
 // BSD-style license that can be found in the LICENSE file.
 
 // This code was auto-generated, is not intended to be edited, and is subject to
 // significant change. Please see the README file for more information.
 
 library engine;
 
 import "dart:math" as math;
@@ skipping 3197 matching lines @@
       } else {
         SourceEntry sourceEntry = _cache.get(source);
         if (sourceEntry != null) {
           sourceEntry.modificationTime =
               _contentCache.getModificationStamp(source);
         }
       }
     } else if (originalContents != null) {
       _incrementalAnalysisCache =
           IncrementalAnalysisCache.clear(_incrementalAnalysisCache, source);
-      _sourceChanged(source);
-      changed = true;
+      String newContents;
+      try {
+        newContents = getContents(source).data;
+        if (newContents == originalContents) {
+          SourceEntry sourceEntry = _cache.get(source);
+          if (sourceEntry != null) {

[Brian Wilkerson, 2015/01/13 19:45:37]

We should get the source entry before reading, because there's no point reading
the file if the source isn't in the cache.

[scheglov, 2015/01/13 20:01:57]

Done.

+            sourceEntry.modificationTime = getModificationStamp(source);

[Brian Wilkerson, 2015/01/13 19:45:37]

We should cache the content in the entry, and we should use the modification
stamp from 'getContents' rather than calling 'getModificationStamp'.

[scheglov, 2015/01/13 20:01:57]

Done.

+          }
+        } else {
+          changed = true;
+        }
+      } catch (e) {
+        changed = true;
+      }
+      if (changed) {
+        _sourceChanged(source);
+      }
     }
     return changed;
   }
 
   /**
    * Create a [GenerateDartErrorsTask] for the given source, marking the verification errors
    * as being in-process. The compilation unit and the library can be the same if the compilation
    * unit is the defining compilation unit of the library.
    *
    * @param unitSource the source for the compilation unit to be verified
@@ skipping 8972 matching lines @@
     if (element.id == _id) {
       result = element;
       throw new _ElementByIdFinderException();
     }
     super.visitElement(element);
   }
 }
 
 class _ElementByIdFinderException {
 }