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

test/upgrade/git/do_not_upgrade_if_unneeded_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("doesn't upgrade one locked Git package's dependencies if it's "
       "not necessary", () {
     ensureGit();
 
     d.git('foo.git', [
       d.libDir('foo'),
       d.libPubspec("foo", "1.0.0", deps: {
         "foo_dep": {"git": "../foo_dep.git"
       }})
     ]).create();
 
     d.git('foo_dep.git', [
       d.libDir('foo_dep'),
       d.libPubspec('foo_dep', '1.0.0')
     ]).create();
 
     d.appDir({"foo": {"git": "../foo.git"}}).create();
 
-    pubGet();
+    pubGet(args: ["--packages-dir"]);
 
     d.dir(packagesPath, [
       d.dir('foo', [
         d.file('foo.dart', 'main() => "foo";')
       ]),
       d.dir('foo_dep', [
         d.file('foo_dep.dart', 'main() => "foo_dep";')
       ])
     ]).validate();
 
     d.git('foo.git', [
       d.libDir('foo', 'foo 2'),
       d.libPubspec("foo", "1.0.0", deps: {
         "foo_dep": {"git": "../foo_dep.git"}
       })
     ]).create();
 
     d.git('foo_dep.git', [
       d.libDir('foo_dep', 'foo_dep 2'),
       d.libPubspec('foo_dep', '1.0.0')
     ]).commit();
 
-    pubUpgrade(args: ['foo']);
+    pubUpgrade(args: ["--packages-dir", 'foo']);
 
     d.dir(packagesPath, [
       d.dir('foo', [
         d.file('foo.dart', 'main() => "foo 2";')
       ]),
       d.dir('foo_dep', [
         d.file('foo_dep.dart', 'main() => "foo_dep";')
       ]),
     ]).validate();
   });
 }