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

test/unknown_source_test.dart

 // Copyright (c) 2012, the Dart project authors.  Please see the AUTHORS d.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 d.file.
 
 import 'dart:convert';
 
 import 'descriptor.dart' as d;
 import 'test_pub.dart';
 
 main() {
@@ skipping 42 matching lines @@
                 'name': 'foo'
               }
             }
           }
         }))
       ]).create();
 
       pubCommand(command);
 
       // Should upgrade to the new one.
-      d.dir(packagesPath, [
-        d.dir("foo", [
-          d.file("foo.dart", 'main() => "foo";')
-        ])
-      ]).validate();
+      d.appPackagesFile({
+        "foo": "../foo"
+      }).validate();
     });
   });
 }