diff -r 9ea2913e7c41 -r c4d63f6740b8 mercurial/transaction.py
--- a/mercurial/transaction.py	Thu Oct 02 00:15:15 2014 -0500
+++ b/mercurial/transaction.py	Wed Oct 01 21:40:44 2014 -0500
@@ -243,7 +243,11 @@
             files = []
             try:
                 for name in filenames:
-                    self.addbackup(name)
+                    # Some files are already backed up when creating the
+                    # localrepo. Until this is properly fixed we disable the
+                    # backup for them.
+                    if name not in ('phaseroots',):
+                        self.addbackup(name)
                     files.append(self.opener(name, 'w', atomictemp=True))
                 genfunc(*files)
             finally: