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

test/upgrade/hosted/upgrade_removed_constraints_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() {
   integration("upgrades dependencies whose constraints have been removed", () {
     servePackages((builder) {
       builder.serve("foo", "1.0.0", deps: {"shared_dep": "any"});
       builder.serve("bar", "1.0.0", deps: {"shared_dep": "<2.0.0"});
       builder.serve("shared_dep", "1.0.0");
       builder.serve("shared_dep", "2.0.0");
     });
 
     d.appDir({"foo": "any", "bar": "any"}).create();
 
     pubUpgrade();
 
-    d.packagesDir({
+    d.appPackagesFile({
       "foo": "1.0.0",
       "bar": "1.0.0",
       "shared_dep": "1.0.0"
     }).validate();
 
     d.appDir({"foo": "any"}).create();
 
     pubUpgrade();
 
-    d.packagesDir({
+    d.appPackagesFile({
       "foo": "1.0.0",
-      "bar": null,
       "shared_dep": "2.0.0"
     }).validate();
   });
 }