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

lib/src/command/upgrade.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 'dart:async';
 
 import '../command.dart';
 import '../log.dart' as log;
 import '../solver/version_solver.dart';
 
@@ skipping 12 matching lines @@
     argParser.addFlag('offline',
         help: 'Use cached packages instead of accessing the network.');
 
     argParser.addFlag('dry-run', abbr: 'n', negatable: false,
         help: "Report what dependencies would change but don't change any.");
 
     argParser.addFlag('precompile', defaultsTo: true,
         help: "Precompile executables and transformed dependencies.");
 
     argParser.addFlag('packages-dir',
-        negatable: true, defaultsTo: true,
+        negatable: true,
         help: "Generate a packages/ directory when installing packages.");
   }
 
   Future run() async {
     await entrypoint.acquireDependencies(SolveType.UPGRADE,
         useLatest: argResults.rest,
         dryRun: argResults['dry-run'],
         precompile: argResults['precompile'],
         packagesDir: argResults['packages-dir']);
 
     if (isOffline) {
       log.warning("Warning: Upgrading when offline may not update you to the "
                   "latest versions of your dependencies.");
     }
   }
 }