Use three-way merge when applying Git patches.

checkout.py

 # coding=utf8
 # Copyright (c) 2012 The Chromium Authors. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 """Manages a project checkout.
 
 Includes support for svn, git-svn and git.
 """
 
 import ConfigParser
@@ skipping 658 matching lines @@
             with open(filepath, 'wb') as f:
               f.write(content)
             stdout.append('Added binary file %d bytes' % len(content))
             cmd = ['add', p.filename]
             if verbose:
               cmd.append('--verbose')
             stdout.append(self._check_output_git(cmd))
           else:
             # No need to do anything special with p.is_new or if not
             # p.diff_hunks. git apply manages all that already.
-            cmd = ['apply', '--index', '-p%s' % p.patchlevel]
+            cmd = ['apply', '--index', '-3', '-p%s' % p.patchlevel]
             if verbose:
               cmd.append('--verbose')
             stdout.append(self._check_output_git(cmd, stdin=p.get(True)))
           for key, value in p.svn_properties:
             # Ignore some known auto-props flags through .subversion/config,
             # bails out on the other ones.
             # TODO(maruel): Read ~/.subversion/config and detect the rules that
             # applies here to figure out if the property will be correctly
             # handled.
             stdout.append('Property %s=%s' % (key, value))
@@ skipping 139 matching lines @@
   def revisions(self, rev1, rev2):
     return self.checkout.revisions(rev1, rev2)
 
   @property
   def project_name(self):
     return self.checkout.project_name
 
   @property
   def project_path(self):
     return self.checkout.project_path