filter-branch: do not consider diverging submodules a 'dirty worktree'

At the end of filter-branch in a non-bare repository, the work tree is
updated with "read-tree -m -u HEAD", to carry the change forward in case
the current branch was rewritten.  In order to avoid losing any local
change during this step, filter-branch refuses to work when there are
local changes in the work tree.

This "read-tree -m -u HEAD" operation does not affect what commit is
checked out in a submodule (iow, it does not touch .git/HEAD in a
submodule checkout), and checking if there is any local change to the
submodule is not useful.

Staged submodules _are_ considered to be 'dirty', however,  as the
"read-tree -m -u HEAD" could result in loss of staged information
otherwise.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

git-filter-branch.sh

@@ -98,7 +98,7 @@ OPTIONS_SPEC=
 . git-sh-setup
 
 if [ "$(is_bare_repository)" = false ]; then
-	git diff-files --quiet &&
+	git diff-files --ignore-submodules --quiet &&
 	git diff-index --cached --quiet HEAD -- ||
 	die "Cannot rewrite branch(es) with a dirty working directory."
 fi