Make "--no-packages-dir" the default.

test/hosted/remove_removed_transitive_dependency_test.dart

 // Copyright (c) 2012, 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.
 
 import '../descriptor.dart' as d;
 import '../test_pub.dart';
 
 main() {
   forBothPubGetAndUpgrade((command) {
     integration("removes a transitive dependency that's no longer depended "
@@ skipping 10 matching lines @@
         builder.serve("bar_dep", "1.0.0");
       });
 
       d.appDir({
         "foo": "any",
         "bar": "any"
       }).create();
 
       pubCommand(command);
 
-      d.packagesDir({
+      d.appPackagesFile({
         "foo": "1.0.0",
         "bar": "1.0.0",
         "shared_dep": "1.0.0",
         "bar_dep": "1.0.0",
       }).validate();
 
       d.appDir({"foo": "any"}).create();
 
       pubCommand(command);
 
-      d.packagesDir({
+      d.appPackagesFile({
         "foo": "1.0.0",
-        "bar": null,
-        "shared_dep": "1.0.0",
-        "bar_dep": null,
+        "shared_dep": "1.0.0"
       }).validate();
     });
   });
 }