Add ApplyChangesStatus to AnalysisContext.applyChanges() and use it in DAS.

pkg/analysis_server/test/analysis_server_test.dart

Index: pkg/analysis_server/test/analysis_server_test.dart
diff --git a/pkg/analysis_server/test/analysis_server_test.dart b/pkg/analysis_server/test/analysis_server_test.dart
index d96439019a90861a74ecb484181b7511de6ec2d5..663c1d84d6be06e30a25d8dcea3f6f67680bc6c1 100644
--- a/pkg/analysis_server/test/analysis_server_test.dart
+++ b/pkg/analysis_server/test/analysis_server_test.dart
@@ -484,6 +484,28 @@ import "../foo/foo.dart";
     });
   }
 
+  test_watch_modifyFile_hasOverlay() async {
+    server.serverServices.add(ServerService.STATUS);
+    // configure the project
+    String projectPath = '/root';
+    String filePath = '/root/test.dart';
+    resourceProvider.newFolder(projectPath);
+    resourceProvider.newFile(filePath, '// 111');
+    server.setAnalysisRoots('0', ['/root'], [], {});
+    await pumpEventQueue();
+    // add overlay
+    server.updateContent('1', {filePath: new AddContentOverlay('// 222')});
+    await pumpEventQueue();
+    // update the file
+    channel.notificationsReceived.clear();
+    resourceProvider.modifyFile(filePath, '// 333');
+    await pumpEventQueue();
+    // the file has an overlay, so the file-system change was ignored
+    expect(channel.notificationsReceived.any((notification) {
+      return notification.event == SERVER_STATUS;
+    }), isFalse);
+  }
+
   void _configureSourceFactory(AnalysisContext context) {
     var resourceUriResolver = new ResourceUriResolver(resourceProvider);
     var packageUriResolver = new PackageMapUriResolver(