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

test/dependency_override_test.dart

 // Copyright (c) 2013, 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:path/path.dart' as path;
 
 import 'descriptor.dart' as d;
 import 'test_pub.dart';
 
 main() {
@@ skipping 12 matching lines @@
             "foo": ">2.0.0"
           },
           "dependency_overrides": {
             "foo": "<3.0.0"
           }
         })
       ]).create();
 
       pubCommand(command);
 
-      d.packagesDir({
+      d.appPackagesFile({
         "foo": "2.0.0"
       }).validate();
     });
 
     integration("treats override as implicit dependency", () {
       servePackages((builder) {
         builder.serve("foo", "1.0.0");
       });
 
       d.dir(appPath, [
         d.pubspec({
           "name": "myapp",
           "dependency_overrides": {
             "foo": "any"
           }
         })
       ]).create();
 
       pubCommand(command);
 
-      d.packagesDir({
+      d.appPackagesFile({
         "foo": "1.0.0"
       }).validate();
     });
 
     integration("ignores other constraints on overridden package", () {
       servePackages((builder) {
         builder.serve("foo", "1.0.0");
         builder.serve("foo", "2.0.0");
         builder.serve("foo", "3.0.0");
         builder.serve("bar", "1.0.0", pubspec: {
           "dependencies": {"foo": "5.0.0-nonexistent"}
         });
       });
 
       d.dir(appPath, [
         d.pubspec({
           "name": "myapp",
           "dependencies": {
             "bar": "any"
           },
           "dependency_overrides": {
             "foo": "<3.0.0"
           }
         })
       ]).create();
 
       pubCommand(command);
 
-      d.packagesDir({
+      d.appPackagesFile({
         "foo": "2.0.0",
         "bar": "1.0.0"
       }).validate();
     });
 
     integration("ignores SDK constraints", () {
       servePackages((builder) {
         builder.serve("foo", "1.0.0", pubspec: {
           "environment": {
             "sdk": "5.6.7-fblthp"
           }
         });
       });
 
       d.dir(appPath, [
         d.pubspec({
           "name": "myapp",
           "dependency_overrides": {
             "foo": "any"
           }
         })
       ]).create();
 
       pubCommand(command);
 
-      d.packagesDir({
+      d.appPackagesFile({
         "foo": "1.0.0"
       }).validate();
     });
 
     integration("warns about overridden dependencies", () {
       servePackages((builder) {
         builder.serve("foo", "1.0.0");
         builder.serve("bar", "1.0.0");
       });
 
@@ skipping 18 matching lines @@
       schedulePub(args: [command.name], output: command.success, error:
           """
           Warning: You are using these overridden dependencies:
           ! bar 1.0.0
           ! baz 0.0.1 from path $bazPath
           ! foo 1.0.0
           """);
     });
   });
 }