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

test/pub_get_and_upgrade_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 'package:pub/src/exit_codes.dart' as exit_codes;
 import 'package:scheduled_test/scheduled_test.dart';
 
 import 'descriptor.dart' as d;
 import 'test_pub.dart';
 
@@ skipping 12 matching lines @@
         d.dir(appPath, [
           d.pubspec({"dependencies": {"foo": null}})
         ]).create();
 
         pubCommand(command,
             error: contains('Missing the required "name" field.'),
             exitCode: exit_codes.DATA);
       });
     });
 
-    integration('adds itself to the packages', () {
-      // The symlink should use the name in the pubspec, not the name of the
+    integration('adds itself to the packages directory and .packages file', () {
+      // The package should use the name in the pubspec, not the name of the
       // directory.
       d.dir(appPath, [
         d.pubspec({"name": "myapp_name"}),
         d.libDir('myapp_name')
       ]).create();
 
-      pubCommand(command);
+      pubCommand(command, args: ["--packages-dir"]);
 
       d.dir(packagesPath, [
         d.dir("myapp_name", [
           d.file('myapp_name.dart', 'main() => "myapp_name";')
         ])
+       ]).validate();
+
+      d.dir("myapp", [
+        d.packagesFile({
+          "myapp_name": "."
+        })
       ]).validate();
     });
 
     integration('does not adds itself to the packages if it has no "lib" '
         'directory', () {
       // The symlink should use the name in the pubspec, not the name of the
       // directory.
       d.dir(appPath, [
         d.pubspec({"name": "myapp_name"}),
       ]).create();
 
-      pubCommand(command);
+      pubCommand(command, args: ["--packages-dir"]);
 
       d.dir(packagesPath, [
         d.nothing("myapp_name")
       ]).validate();
     });
 
     integration('does not add a package if it does not have a "lib" '
         'directory', () {
       // Using a path source, but this should be true of all sources.
       d.dir('foo', [
         d.libPubspec('foo', '0.0.0-not.used')
       ]).create();
 
       d.dir(appPath, [
         d.appPubspec({"foo": {"path": "../foo"}})
       ]).create();
 
-      pubCommand(command);
+      pubCommand(command, args: ["--packages-dir"]);
 
       d.packagesDir({"foo": null}).validate();
     });
 
     integration('reports a solver failure', () {
       // myapp depends on foo and bar which both depend on baz with mismatched
       // descriptions.
       d.dir('deps', [
         d.dir('foo', [
           d.pubspec({"name": "foo", "dependencies": {
@@ skipping 45 matching lines @@
           }
         })
       ]).create();
 
       pubCommand(command,
           error: contains('A package may not list itself as a dependency.'),
           exitCode: exit_codes.DATA);
     });
   });
 }