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

test/upgrade/hosted/unlock_if_necessary_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 one locked pub server package's dependencies if it's "
       "necessary", () {
     servePackages((builder) {
       builder.serve("foo", "1.0.0", deps: {"foo_dep": "any"});
       builder.serve("foo_dep", "1.0.0");
     });
 
     d.appDir({"foo": "any"}).create();
 
     pubGet();
 
-    d.packagesDir({
+    d.appPackagesFile({
       "foo": "1.0.0",
       "foo_dep": "1.0.0"
     }).validate();
 
     globalPackageServer.add((builder) {
       builder.serve("foo", "2.0.0", deps: {"foo_dep": ">1.0.0"});
       builder.serve("foo_dep", "2.0.0");
     });
 
     pubUpgrade(args: ['foo']);
 
-    d.packagesDir({
+    d.appPackagesFile({
       "foo": "2.0.0",
       "foo_dep": "2.0.0"
     }).validate();
   });
 }