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

test/upgrade/git/upgrade_to_nonexistent_pubspec_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 Git packages to a nonexistent pubspec", () {
     ensureGit();
 
     var repo = d.git('foo.git', [
       d.libDir('foo'),
       d.libPubspec('foo', '1.0.0')
     ]);
     repo.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";')
       ])
     ]).validate();
 
     repo.runGit(['rm', 'pubspec.yaml']);
     repo.runGit(['commit', '-m', 'delete']);
 
-    pubUpgrade(error: new RegExp(r'Could not find a file named "pubspec.yaml" '
-        r'in [^\n]*\.'));
+    pubUpgrade(
+        args: ["--packages-dir"],
+        error: new RegExp(r'Could not find a file named "pubspec.yaml" '
+            r'in [^\n]*\.'));
 
     d.dir(packagesPath, [
       d.dir('foo', [
         d.file('foo.dart', 'main() => "foo";')
       ])
     ]).validate();
   });
 }