patch, 3 partssane rebase/stash support with submodules

Documentation/diff-options.txt, diff.c, diff.h

diff --git a/Documentation/diff-options.txt b/Documentation/diff-options.txt
index 13234fa..859d679 100644
--- a/Documentation/diff-options.txt
+++ b/Documentation/diff-options.txt
@@ -228,6 +228,9 @@ endif::git-format-patch[]
 --no-ext-diff::
 	Disallow external diff drivers.
 
+--ignore-submodules::
+	Ignore changes to submodules in the diff generation.
+
 --src-prefix=<prefix>::
 	Show the given source prefix instead of "a/".
 
diff --git a/diff.c b/diff.c
index 439d474..d57bc29 100644
--- a/diff.c
+++ b/diff.c
@@ -2496,6 +2496,8 @@ int diff_opt_parse(struct diff_options *options, const char **av, int ac)
 		DIFF_OPT_SET(options, ALLOW_EXTERNAL);
 	else if (!strcmp(arg, "--no-ext-diff"))
 		DIFF_OPT_CLR(options, ALLOW_EXTERNAL);
+	else if (!strcmp(arg, "--ignore-submodules"))
+		DIFF_OPT_SET(options, IGNORE_SUBMODULES);
 
 	/* misc options */
 	else if (!strcmp(arg, "-z"))
@@ -3355,6 +3357,9 @@ void diff_addremove(struct diff_options *options,
 	char concatpath[PATH_MAX];
 	struct diff_filespec *one, *two;
 
+	if (DIFF_OPT_TST(options, IGNORE_SUBMODULES) && S_ISGITLINK(mode))
+		return;
+
 	/* This may look odd, but it is a preparation for
 	 * feeding "there are unchanged files which should
 	 * not produce diffs, but when you are doing copy
@@ -3399,6 +3404,10 @@ void diff_change(struct diff_options *options,
 	char concatpath[PATH_MAX];
 	struct diff_filespec *one, *two;
 
+	if (DIFF_OPT_TST(options, IGNORE_SUBMODULES) && S_ISGITLINK(old_mode)
+			&& S_ISGITLINK(new_mode))
+		return;
+
 	if (DIFF_OPT_TST(options, REVERSE_DIFF)) {
 		unsigned tmp;
 		const unsigned char *tmp_c;
diff --git a/diff.h b/diff.h
index 3a02d38..1dfe1f9 100644
--- a/diff.h
+++ b/diff.h
@@ -63,6 +63,7 @@ typedef void (*diff_format_fn_t)(struct diff_queue_struct *q,
 #define DIFF_OPT_REVERSE_DIFF        (1 << 15)
 #define DIFF_OPT_CHECK_FAILED        (1 << 16)
 #define DIFF_OPT_RELATIVE_NAME       (1 << 17)
+#define DIFF_OPT_IGNORE_SUBMODULES   (1 << 18)
 #define DIFF_OPT_TST(opts, flag)    ((opts)->flags & DIFF_OPT_##flag)
 #define DIFF_OPT_SET(opts, flag)    ((opts)->flags |= DIFF_OPT_##flag)
 #define DIFF_OPT_CLR(opts, flag)    ((opts)->flags &= ~DIFF_OPT_##flag)

Documentation/git-update-index.txt, builtin-update-index.c, cache.h, read-cache.c

diff --git a/Documentation/git-update-index.txt b/Documentation/git-update-index.txt
index 66be18e..0664060 100644
--- a/Documentation/git-update-index.txt
+++ b/Documentation/git-update-index.txt
@@ -15,6 +15,7 @@ SYNOPSIS
 	     [--cacheinfo <mode> <object> <file>]\*
 	     [--chmod=(+|-)x]
 	     [--assume-unchanged | --no-assume-unchanged]
+	     [--ignore-submodules]
 	     [--really-refresh] [--unresolve] [--again | -g]
 	     [--info-only] [--index-info]
 	     [-z] [--stdin]
@@ -54,6 +55,10 @@ OPTIONS
         default behavior is to error out.  This option makes
         git-update-index continue anyway.
 
+--ignore-submodules:
+	Do not try to update submodules.  This option is only respected
+	when passed before --refresh.
+
 --unmerged::
         If --refresh finds unmerged changes in the index, the default
         behavior is to error out.  This option makes git-update-index
diff --git a/builtin-update-index.c b/builtin-update-index.c
index a8795d3..d4c85c0 100644
--- a/builtin-update-index.c
+++ b/builtin-update-index.c
@@ -593,6 +593,10 @@ int cmd_update_index(int argc, const char **argv, const char *prefix)
 				refresh_flags |= REFRESH_QUIET;
 				continue;
 			}
+			if (!strcmp(path, "--ignore-submodules")) {
+				refresh_flags |= REFRESH_IGNORE_SUBMODULES;
+				continue;
+			}
 			if (!strcmp(path, "--add")) {
 				allow_add = 1;
 				continue;
diff --git a/cache.h b/cache.h
index c761915..3d4e8e7 100644
--- a/cache.h
+++ b/cache.h
@@ -393,6 +393,7 @@ extern void fill_stat_cache_info(struct cache_entry *ce, struct stat *st);
 #define REFRESH_UNMERGED	0x0002	/* allow unmerged */
 #define REFRESH_QUIET		0x0004	/* be quiet about it */
 #define REFRESH_IGNORE_MISSING	0x0008	/* ignore non-existent */
+#define REFRESH_IGNORE_SUBMODULES	0x0008	/* ignore submodules */
 extern int refresh_index(struct index_state *, unsigned int flags, const char **pathspec, char *seen);
 
 struct lock_file {
diff --git a/read-cache.c b/read-cache.c
index 8b467f8..bc03981 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -942,6 +942,7 @@ int refresh_index(struct index_state *istate, unsigned int flags, const char **p
 	int allow_unmerged = (flags & REFRESH_UNMERGED) != 0;
 	int quiet = (flags & REFRESH_QUIET) != 0;
 	int not_new = (flags & REFRESH_IGNORE_MISSING) != 0;
+	int ignore_submodules = (flags & REFRESH_IGNORE_SUBMODULES) != 0;
 	unsigned int options = really ? CE_MATCH_IGNORE_VALID : 0;
 
 	for (i = 0; i < istate->cache_nr; i++) {
@@ -949,6 +950,9 @@ int refresh_index(struct index_state *istate, unsigned int flags, const char **p
 		int cache_errno = 0;
 
 		ce = istate->cache[i];
+		if (ignore_submodules && S_ISGITLINK(ce->ce_mode))
+			continue;
+
 		if (ce_stage(ce)) {
 			while ((i < istate->cache_nr) &&
 			       ! strcmp(istate->cache[i]->name, ce->name))

git-rebase--interactive.sh, git-rebase.sh, git-stash.sh, t/t7402-submodule-rebase.sh

diff --git a/git-rebase--interactive.sh b/git-rebase--interactive.sh
index 2a01182..a9daa1b 100755
--- a/git-rebase--interactive.sh
+++ b/git-rebase--interactive.sh
@@ -56,9 +56,9 @@ output () {
 require_clean_work_tree () {
 	# test if working tree is dirty
 	git rev-parse --verify HEAD > /dev/null &&
-	git update-index --refresh &&
-	git diff-files --quiet &&
-	git diff-index --cached --quiet HEAD -- ||
+	git update-index --ignore-submodules --refresh &&
+	git diff-files --quiet --ignore-submodules &&
+	git diff-index --cached --quiet HEAD --ignore-submodules -- ||
 	die "Working tree is dirty"
 }
 
@@ -526,11 +526,12 @@ do
 		# Sanity check
 		git rev-parse --verify HEAD >/dev/null ||
 			die "Cannot read HEAD"
-		git update-index --refresh && git diff-files --quiet ||
+		git update-index --ignore-submodules --refresh &&
+			git diff-files --quiet --ignore-submodules ||
 			die "Working tree is dirty"
 
 		# do we have anything to commit?
-		if git diff-index --cached --quiet HEAD --
+		if git diff-index --cached --quiet --ignore-submodules HEAD --
 		then
 			: Nothing to commit -- skip this
 		else
diff --git a/git-rebase.sh b/git-rebase.sh
index 68855c1..dd7dfe1 100755
--- a/git-rebase.sh
+++ b/git-rebase.sh
@@ -60,7 +60,7 @@ continue_merge () {
 	fi
 
 	cmt=`cat "$dotest/current"`
-	if ! git diff-index --quiet HEAD --
+	if ! git diff-index --quiet --ignore-submodules HEAD --
 	then
 		if ! git commit --no-verify -C "$cmt"
 		then
@@ -150,7 +150,7 @@ while test $# != 0
 do
 	case "$1" in
 	--continue)
-		git diff-files --quiet || {
+		git diff-files --quiet --ignore-submodules || {
 			echo "You must edit all merge conflicts and then"
 			echo "mark them as resolved using git add"
 			exit 1
@@ -282,8 +282,8 @@ else
 fi
 
 # The tree must be really really clean.
-git update-index --refresh || exit
-diff=$(git diff-index --cached --name-status -r HEAD --)
+git update-index --ignore-submodules --refresh || exit
+diff=$(git diff-index --cached --name-status -r --ignore-submodules HEAD --)
 case "$diff" in
 ?*)	echo "cannot rebase: your index is not up-to-date"
 	echo "$diff"
diff --git a/git-stash.sh b/git-stash.sh
index c2b6820..4938ade 100755
--- a/git-stash.sh
+++ b/git-stash.sh
@@ -15,8 +15,8 @@ trap 'rm -f "$TMP-*"' 0
 ref_stash=refs/stash
 
 no_changes () {
-	git diff-index --quiet --cached HEAD -- &&
-	git diff-files --quiet
+	git diff-index --quiet --cached HEAD --ignore-submodules -- &&
+	git diff-files --quiet --ignore-submodules
 }
 
 clear_stash () {
@@ -130,7 +130,7 @@ show_stash () {
 }
 
 apply_stash () {
-	git diff-files --quiet ||
+	git diff-files --quiet --ignore-submodules ||
 		die 'Cannot restore on top of a dirty state'
 
 	unstash_index=
diff --git a/t/t7402-submodule-rebase.sh b/t/t7402-submodule-rebase.sh
new file mode 100755
index 0000000..5becb3e
--- /dev/null
+++ b/t/t7402-submodule-rebase.sh
@@ -0,0 +1,92 @@
+#!/bin/sh
+#
+# Copyright (c) 2008 Johannes Schindelin
+#
+
+test_description='Test rebasing and stashing with dirty submodules'
+
+. ./test-lib.sh
+
+test_expect_success setup '
+
+	echo file > file &&
+	git add file &&
+	test_tick &&
+	git commit -m initial &&
+	git clone . submodule &&
+	git add submodule &&
+	test_tick &&
+	git commit -m submodule &&
+	echo second line >> file &&
+	(cd submodule && git pull) &&
+	test_tick &&
+	git commit -m file-and-submodule -a
+
+'
+
+test_expect_success 'rebase with a dirty submodule' '
+
+	(cd submodule &&
+	 echo 3rd line >> file &&
+	 test_tick &&
+	 git commit -m fork -a) &&
+	echo unrelated >> file2 &&
+	git add file2 &&
+	test_tick &&
+	git commit -m unrelated file2 &&
+	echo other line >> file &&
+	test_tick &&
+	git commit -m update file &&
+	CURRENT=$(cd submodule && git rev-parse HEAD) &&
+	EXPECTED=$(git rev-parse HEAD~2:submodule) &&
+	GIT_TRACE=1 git rebase --onto HEAD~2 HEAD^ &&
+	STORED=$(git rev-parse HEAD:submodule) &&
+	test $EXPECTED = $STORED &&
+	test $CURRENT = $(cd submodule && git rev-parse HEAD)
+
+'
+
+cat > fake-editor.sh << \EOF
+#!/bin/sh
+echo $EDITOR_TEXT
+EOF
+chmod a+x fake-editor.sh
+
+test_expect_success 'interactive rebase with a dirty submodule' '
+
+	test submodule = $(git diff --name-only) &&
+	HEAD=$(git rev-parse HEAD) &&
+	GIT_EDITOR="\"$(pwd)/fake-editor.sh\"" EDITOR_TEXT="pick $HEAD" \
+		git rebase -i HEAD^ &&
+	test submodule = $(git diff --name-only)
+
+'
+
+test_expect_success 'rebase with dirty file and submodule fails' '
+
+	echo yet another line >> file &&
+	test_tick &&
+	git commit -m next file &&
+	echo rewrite > file &&
+	test_tick &&
+	git commit -m rewrite file &&
+	echo dirty > file &&
+	! git rebase --onto HEAD~2 HEAD^
+
+'
+
+test_expect_success 'stash with a dirty submodule' '
+
+	echo new > file &&
+	CURRENT=$(cd submodule && git rev-parse HEAD) &&
+	git stash &&
+	test new != $(cat file) &&
+	test submodule = $(git diff --name-only) &&
+	test $CURRENT = $(cd submodule && git rev-parse HEAD) &&
+	git stash apply &&
+	test new = $(cat file) &&
+	test $CURRENT = $(cd submodule && git rev-parse HEAD)
+
+'
+
+test_done