diff -r 646a224ca76a -r b3bf6d72fea5 src/Pure/System/options.scala
--- a/src/Pure/System/options.scala	Fri Aug 30 21:14:38 2013 +0200
+++ b/src/Pure/System/options.scala	Fri Aug 30 22:22:07 2013 +0200
@@ -66,7 +66,6 @@
   private val OPTIONS = Path.explode("etc/options")
   private val PREFS_DIR = Path.explode("$ISABELLE_HOME_USER/etc")
   private val PREFS = PREFS_DIR + Path.basic("preferences")
-  private val PREFS_BACKUP = PREFS_DIR + Path.basic("preferences~")
 
   lazy val options_syntax =
     Outer_Syntax.init() + ":" + "=" + "--" +
@@ -359,8 +358,7 @@
         .map({ case (x, y, z) => x + " = " + Outer_Syntax.quote_string(y) + z + "\n" }).mkString
 
     Isabelle_System.mkdirs(Options.PREFS_DIR)
-    Options.PREFS.file renameTo Options.PREFS_BACKUP.file
-    File.write(Options.PREFS,
+    File.write_backup(Options.PREFS,
       "(* generated by Isabelle " + Calendar.getInstance.getTime + " *)\n\n" + prefs)
   }
 }