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

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

Index: pkg/analyzer/lib/src/generated/engine.dart
diff --git a/pkg/analyzer/lib/src/generated/engine.dart b/pkg/analyzer/lib/src/generated/engine.dart
index 173735221af803dc8873784685a3a38a83ec1ed8..75ec85de4154bd40fe5f33d971f997071ee0c2b3 100644
--- a/pkg/analyzer/lib/src/generated/engine.dart
+++ b/pkg/analyzer/lib/src/generated/engine.dart
@@ -3215,8 +3215,23 @@ class AnalysisContextImpl implements InternalAnalysisContext {
     } 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;
   }