Include node's config.gypi in atom-shell.

Removed 3 commits of our node fork.

script/bootstrap.py

@@ -19,14 +19,14 @@ def main():
   os.chdir(SOURCE_ROOT)
 
   args = parse_args()
-  update_submodules()
-  bootstrap_brightray(args.url)
-
   if not args.skip_network:
+    update_submodules()
     update_node_modules()
+    bootstrap_brightray(args.url)
     if sys.platform == 'cygwin':
       update_win32_python()
 
+  touch_config_gypi()
   update_atom_shell()
 
 
@@ -68,6 +68,12 @@ def update_win32_python():
         subprocess.check_call(['git', 'pull', '--rebase'])
 
 
+def touch_config_gypi():
+  config_gypi = os.path.join(SOURCE_ROOT, 'vendor', 'node', 'config.gypi')
+  with open(config_gypi, 'w+') as f:
+    f.truncate(0)
+
+
 def update_atom_shell():
   update = os.path.join(SOURCE_ROOT, 'script', 'update.py')
   subprocess.check_call([sys.executable, update])