diff --git a/lib/Tools/setup b/lib/Tools/setup
--- a/lib/Tools/setup
+++ b/lib/Tools/setup
@@ -1,110 +1,116 @@
 #!/usr/bin/env bash
 #
 # Author: Makarius
 #
 # DESCRIPTION: setup for Isabelle repository clone or repository archive
 
 
 ## diagnostics
 
 PRG="$(basename "$0")"
 
 function usage()
 {
   echo
   echo "Usage: isabelle $PRG [OPTIONS]"
   echo
   echo "  Options are:"
   echo "    -r REV       explicit Mercurial version"
+  echo "    -C           enforce clean update of working directory (no backup!)"
   echo "    -V PATH      version from explicit file or directory (file \"ISABELLE_VERSION\")"
   echo
   echo "  Setup the current ISABELLE_HOME directory, which needs to be a"
   echo "  repository clone (all versions) or repository archive (fixed version)."
   echo
   exit 1
 }
 
 function fail()
 {
   echo "$1" >&2
   exit 2
 }
 
 
 ## process command line
 
 #options
 
-VERSION_REV=""
+CLEAN=""
 VERSION_PATH=""
+VERSION_REV=""
 
-while getopts "r:V:" OPT
+while getopts "CV:r:" OPT
 do
   case "$OPT" in
-    r)
-      VERSION_REV="$OPTARG"
+    C)
+      CLEAN="--clean"
       ;;
     V)
       VERSION_PATH="$OPTARG"
       ;;
+    r)
+      VERSION_REV="$OPTARG"
+      ;;
     \?)
       usage
       ;;
   esac
 done
 
 shift $(($OPTIND - 1))
 
 
 # args
 
 [ "$#" -ne 0 ] && usage
 
 
 ## main
 
 if [ -z "$VERSION_REV" -a -z "$VERSION_PATH" ]; then
   isabelle components -I && isabelle components -a
 elif [ -n "$VERSION_REV" -a -n "$VERSION_PATH" ]; then
   fail "Duplicate version specification (options -r and -V)"
 elif [ ! -d "$ISABELLE_HOME/.hg" ]; then
   fail "Not a repository clone: cannot specify version"
 else
   export REV=""
   if [ -n "$VERSION_REV" ]; then
     REV="$VERSION_REV"
   elif [ -f "$VERSION_PATH" ]; then
     REV="$(cat "$VERSION_PATH")"
   elif [ -d "$VERSION_PATH" ]; then
     if [ -f "$VERSION_PATH/ISABELLE_VERSION" ]; then
       REV="$(cat "$VERSION_PATH/ISABELLE_VERSION")"
     else
       fail "Missing file \"$VERSION_PATH/ISABELLE_VERSION\""
     fi
   else
     fail "Missing file \"$VERSION_PATH\""
   fi
 
   export LANG=C
   export HGPLAIN=
 
   if "${HG:-hg}" id -r "$REV" >/dev/null 2>/dev/null
   then
-    export PULL=""
+    PULL=""
   else
-    export PULL=true
+    PULL=true
   fi
 
   isabelle components -I
 
   #Atomic exec: avoid inplace update of running script!
+  export CLEAN PULL
   exec bash -c '
     set -e
     if [ -n "$PULL" ]; then
       "${HG:-hg}" pull -r "$REV"
     fi
-    "${HG:-hg}" update -r "$REV"
+    "${HG:-hg}" update -r "$REV" $CLEAN
+    isabelle components -a
     "${HG:-hg}" log -r "$REV"
-    isabelle components -a
   '
 fi