Create a separate packages directory for running pub.

utils/pub/pub.gyp

 # 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.
 
 {
   'targets': [
     {
       'target_name': 'pub',
       'type': 'none',
       'dependencies': [
         '../../runtime/dart-runtime.gyp:dart',
-        '../../pkg/pkg.gyp:pkg_packages',
+        '../../pkg/pkg.gyp:pub_packages',
         '../../pkg/pkg_files.gyp:pkg_files_stamp',
         '../../utils/compiler/compiler.gyp:dart2js_files_stamp',
         'pub_files_stamp'
       ],
       'actions': [
         {
           'action_name': 'generate_pub_snapshot',
           'inputs': [
             '<(PRODUCT_DIR)/<(EXECUTABLE_PREFIX)dart<(EXECUTABLE_SUFFIX)',
             '../../sdk/lib/_internal/libraries.dart',
             '<(SHARED_INTERMEDIATE_DIR)/pub_files.stamp',
             '<(SHARED_INTERMEDIATE_DIR)/dart2js_files.stamp',

[ricow1, 2014/08/12 05:57:21]

Does pub need pub_packages target to be build before pub is build?
If so, you need to have this in the inputs as well:
'<(SHARED_INTERMEDIATE_DIR)/pub_packages.stamp'

Generally speaking, a dependency does not imply any particular build order
(because in a normal c world you don't have that, you do the linking at the end)

[nweiz, 2014/08/12 23:12:18]

Done.

             '<(SHARED_INTERMEDIATE_DIR)/pkg_files.stamp',
           ],
           'outputs': [
             '<(SHARED_INTERMEDIATE_DIR)/pub.dart.snapshot',
           ],
           'action': [
             '<(PRODUCT_DIR)/<(EXECUTABLE_PREFIX)dart<(EXECUTABLE_SUFFIX)',
-            '--package-root=<(PRODUCT_DIR)/packages/',
+            '--package-root=<(PRODUCT_DIR)/pub_packages/',
             '--snapshot=<(SHARED_INTERMEDIATE_DIR)/pub.dart.snapshot',
             '../../sdk/lib/_internal/pub/bin/pub.dart',
           ],
         },
       ],
     },
     # Other targets depend on pub files, but have to many inputs, which causes
     # issues on some platforms.
     # This target lists all the files in sdk/lib/_internal/pub,
     # and creates a single pub_files.stamp
@@ skipping 15 matching lines @@
             'python', '../../tools/create_timestamp_file.py',
             '<@(_outputs)',
           ],
         },
       ],
     }
 
 
   ],
 }