Add submodule test harness

index 158e10a..546f0a6 100644
@@ -489,6 +489,17 @@ test_path_is_dir () {
 	fi
 }
 
+# Check if the directory exists and is empty as expected, barf otherwise.
+test_dir_is_empty () {
+	test_path_is_dir "$1" &&
+	if test "$(ls -a1 "$1" | egrep -v '^\.\.?$')"
+	then
+		echo "Directory '$1' is not empty, it contains:"
+		ls -la "$1"
+		return 1
+	fi
+}
+
 test_path_is_missing () {
 	if [ -e "$1" ]
 	then

index c617c82..acd9a55 100644
@@ -489,6 +489,17 @@ test_path_is_dir () {
 	fi
 }
 
+# Check if the directory exists and is empty as expected, barf otherwise.
+test_dir_is_empty () {
+	test_path_is_dir "$1" &&
+	if test -n "$(ls -a1 "$1" | egrep -v '^\.\.?$')"
+	then
+		echo "Directory '$1' is not empty, it contains:"
+		ls -la "$1"
+		return 1
+	fi
+}
+
 test_path_is_missing () {
 	if [ -e "$1" ]
 	then

new file mode 100755
index 0000000..c6c842a
@@ -0,0 +1,630 @@
+# Create a submodule layout used for all tests below.
+#
+# The following use cases are covered:
+# - New submodule (no_submodule => add_sub1)
+# - Removed submodule (add_sub1 => remove_sub1)
+# - Updated submodule (add_sub1 => modify_sub1)
+# - Submodule updated to invalid commit (add_sub1 => invalid_sub1)
+# - Submodule updated from invalid commit (invalid_sub1 => valid_sub1)
+# - Submodule replaced by tracked files in directory (add_sub1 =>
+#   replace_sub1_with_directory)
+# - Directory containing tracked files replaced by submodule
+#   (replace_sub1_with_directory => replace_directory_with_sub1)
+# - Submodule replaced by tracked file with the same name (add_sub1 =>
+#   replace_sub1_with_file)
+# - Tracked file replaced by submodule (replace_sub1_with_file =>
+#   replace_file_with_sub1)
+#
+#                   --O-----O
+#                  /  ^     replace_directory_with_sub1
+#                 /   replace_sub1_with_directory
+#                /----O
+#               /     ^
+#              /      modify_sub1
+#      O------O-------O
+#      ^      ^\      ^
+#      |      | \     remove_sub1
+#      |      |  -----O-----O
+#      |      |   \   ^     replace_file_with_sub1
+#      |      |    \  replace_sub1_with_file
+#      |   add_sub1 --O-----O
+# no_submodule        ^     valid_sub1
+#                     invalid_sub1
+#
+create_lib_submodule_repo () {
+	git init submodule_update_repo &&
+	(
+		cd submodule_update_repo &&
+		echo "expect" >>.gitignore &&
+		echo "actual" >>.gitignore &&
+		echo "x" >file1 &&
+		echo "y" >file2 &&
+		git add .gitignore file1 file2 &&
+		git commit -m "Base" &&
+		git branch "no_submodule" &&
+
+		git checkout -b "add_sub1" &&
+		git submodule add ./. sub1 &&
+		git config -f .gitmodules submodule.sub1.ignore all &&
+		git config submodule.sub1.ignore all &&
+		git add .gitmodules &&
+		git commit -m "Add sub1" &&
+		git checkout -b remove_sub1 &&
+		git revert HEAD &&
+
+		git checkout -b "modify_sub1" "add_sub1" &&
+		git submodule update &&
+		(
+			cd sub1 &&
+			git fetch &&
+			git checkout -b "modifications" &&
+			echo "z" >file2 &&
+			echo "x" >file3 &&
+			git add file2 file3 &&
+			git commit -m "modified file2 and added file3" &&
+			git push origin modifications
+		) &&
+		git add sub1 &&
+		git commit -m "Modify sub1" &&
+
+		git checkout -b "replace_sub1_with_directory" "add_sub1" &&
+		git submodule update &&
+		(
+			cd sub1 &&
+			git checkout modifications
+		) &&
+		git rm --cached sub1 &&
+		rm sub1/.git* &&
+		git config -f .gitmodules --remove-section "submodule.sub1" &&
+		git add .gitmodules sub1/* &&
+		git commit -m "Replace sub1 with directory" &&
+		git checkout -b replace_directory_with_sub1 &&
+		git revert HEAD &&
+
+		git checkout -b "replace_sub1_with_file" "add_sub1" &&
+		git rm sub1 &&
+		echo "content" >sub1 &&
+		git add sub1 &&
+		git commit -m "Replace sub1 with file" &&
+		git checkout -b replace_file_with_sub1 &&
+		git revert HEAD &&
+
+		git checkout -b "invalid_sub1" "add_sub1" &&
+		git update-index --cacheinfo 160000 0123456789012345678901234567890123456789 sub1 &&
+		git commit -m "Invalid sub1 commit" &&
+		git checkout -b valid_sub1 &&
+		git revert HEAD &&
+		git checkout master
+	)
+}
+
+# Helper function to replace gitfile with .git directory
+replace_gitfile_with_git_dir () {
+	(
+		cd "$1" &&
+		git_dir="$(git rev-parse --git-dir)" &&
+		rm -f .git &&
+		cp -a "$git_dir" .git &&
+		GIT_WORK_TREE=. git config --unset core.worktree
+	)
+}
+
+# Test that the .git directory in the submodule is unchanged (except for the
+# core.worktree setting)
+test_git_directory_is_unchanged () {
+	(
+		cd "$1" &&
+		git config core.worktree "../../../$1"
+	) &&
+	git diff -r ".git/modules/$1" "$1/.git" &&
+	(
+		cd "$1" &&
+		GIT_WORK_TREE=. git config --unset core.worktree
+	)
+}
+
+# Helper function to be executed at the start of every test below, it sets up
+# the submodule repo if it doesn't exist and configures the most problematic
+# settings for diff.ignoreSubmodules.
+prolog () {
+	(test -d submodule_update_repo || create_lib_submodule_repo) &&
+	test_config_global diff.ignoreSubmodules all &&
+	test_config diff.ignoreSubmodules all
+}
+
+# Helper function to bring work tree back into the state given by the
+# commit. This includes trying to populate sub1 accordingly if it exists and
+# should be updated to an existing commit.
+reset_work_tree_to () {
+	rm -rf submodule_update &&
+	git clone submodule_update_repo submodule_update &&
+	(
+		cd submodule_update &&
+		rm -rf sub1 &&
+		git checkout -f "$1" &&
+		git status -u -s >actual &&
+		test_must_be_empty actual &&
+		sha1=$(git ls-tree HEAD "sub1" 2>/dev/null | grep 160000 | tr '\t' ' ' | cut -d ' ' -f3) &&
+		if test -n "$sha1" &&
+		   test $(cd "sub1" && git rev-parse --verify "$sha1^{commit}")
+		then
+			git submodule update --init --recursive "sub1"
+		fi
+	)
+}
+
+# Test that the superproject contains the content according to commit "$1"
+# (the work tree must match the index for everything but submodules but the
+# index must exactly match the given commit including any submodule SHA-1s).
+test_superproject_content () {
+	git diff-index --cached "$1" >actual &&
+	test_must_be_empty actual &&
+	git diff-files --ignore-submodules >actual &&
+	test_must_be_empty actual
+}
+
+# Test that the given submodule at path "$1" contains the content according
+# to the submodule commit recorded in the superproject's commit "$2"
+test_submodule_content () {
+	if test $# != 2
+	then
+		echo "test_submodule_content needs two arguments"
+		return 1
+	fi &&
+	submodule="$1" &&
+	commit="$2" &&
+	test -d "$submodule"/ &&
+	if ! test -f "$submodule"/.git && ! test -d "$submodule"/.git
+	then
+		echo "Submodule $submodule is not populated"
+		return 1
+	fi &&
+	sha1=$(git ls-tree "$commit" "$submodule" 2>/dev/null | tr '\t' ' ' | cut -d ' ' -f3) &&
+	if test -z "$sha1"
+	then
+		echo "Couldn't retrieve SHA-1 of $submodule for $commit"
+		return 1
+	fi &&
+	(
+		cd "$submodule" &&
+		git status -u -s >actual &&
+		test_must_be_empty actual &&
+		git diff "$sha1" >actual &&
+		test_must_be_empty actual
+	)
+}
+
+# Test that the following transitions are correctly handled:
+# - Updated submodule
+# - New submodule
+# - Removed submodule
+# - Directory containing tracked files replaced by submodule
+# - Submodule replaced by tracked files in directory
+# - Submodule replaced by tracked file with the same name
+# - tracked file replaced by submodule
+#
+# The default is that submodule contents aren't changed until "git submodule
+# update" is run. And even then that command doesn't delete the work tree of
+# a removed submodule.
+#
+# Removing a submodule containing a .git directory must fail even when forced
+# to protect the history!
+#
+
+# Test that submodule contents are currently not updated when switching
+# between commits that change a submodule.
+test_submodule_switch () {
+	command="$1"
+	######################### Appearing submodule #########################
+	# Switching to a commit letting a submodule appear creates empty dir ...
+	test_expect_success "$command: added submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... and doesn't care if it already exists ...
+	test_expect_success "$command: added submodule leaves existing empty directory alone" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			mkdir sub1 &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... unless there is an untracked file in its place.
+	test_expect_success "$command: added submodule doesn't remove untracked unignored file with same name" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			echo -n >sub1 &&
+			test_must_fail $command add_sub1 &&
+			test_superproject_content origin/no_submodule &&
+			test_must_be_empty sub1
+		)
+	'
+	# Replacing a tracked file with a submodule produces an empty
+	# directory ...
+	test_expect_success "$command: replace tracked file with submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_file &&
+		(
+			cd submodule_update &&
+			git branch -t replace_file_with_sub1 origin/replace_file_with_sub1 &&
+			$command replace_file_with_sub1 &&
+			test_superproject_content origin/replace_file_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_file_with_sub1
+		)
+	'
+	# ... as does removing a directory with tracked files with a
+	# submodule.
+	test_expect_success "$command: replace directory with submodule" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_directory &&
+		(
+			cd submodule_update &&
+			git branch -t replace_directory_with_sub1 origin/replace_directory_with_sub1 &&
+			$command replace_directory_with_sub1 &&
+			test_superproject_content origin/replace_directory_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_directory_with_sub1
+		)
+	'
+
+	######################## Disappearing submodule #######################
+	# Removing a submodule doesn't remove its work tree ...
+	test_expect_success "$command: removed submodule leaves submodule directory and its contents in place" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_success "$command: removed submodule leaves submodule containing a .git directory alone" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			replace_gitfile_with_git_dir sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1
+		)
+	'
+	# Replacing a submodule with files in a directory must fail as the
+	# submodule work tree isn't removed ...
+	test_expect_success "$command: replace submodule with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_success "$command: replace submodule containing a .git directory with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1
+		)
+	'
+	# Replacing it with a file must fail as it could throw away any local
+	# work tree changes ...
+	test_expect_failure "$command: replace submodule with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... or even destroy unpushed parts of submodule history if that
+	# still uses a .git directory.
+	test_expect_failure "$command: replace submodule containing a .git directory with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1
+		)
+	'
+
+	########################## Modified submodule #########################
+	# Updating a submodule sha1 doesn't update the submodule's work tree
+	test_expect_success "$command: modified submodule does not update submodule work tree" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t modify_sub1 origin/modify_sub1 &&
+			$command modify_sub1 &&
+			test_superproject_content origin/modify_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			git submodule update &&
+			test_submodule_content sub1 origin/modify_sub1
+		)
+	'
+
+	# Updating a submodule to an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will fail
+	test_expect_success "$command: modified submodule does not update submodule work tree to invalid commit" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t invalid_sub1 origin/invalid_sub1 &&
+			$command invalid_sub1 &&
+			test_superproject_content origin/invalid_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_must_fail git submodule update &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Updating a submodule from an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will succeed
+	test_expect_success "$command: modified submodule does not update submodule work tree from invalid commit" '
+		prolog &&
+		reset_work_tree_to invalid_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t valid_sub1 origin/valid_sub1 &&
+			$command valid_sub1 &&
+			test_superproject_content origin/valid_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/valid_sub1
+		)
+	'
+}
+
+# Test that submodule contents are currently not updated when switching
+# between commits that change a submodule, but throwing away local changes in
+# the superproject is allowed.
+test_submodule_forced_switch () {
+	command="$1"
+	######################### Appearing submodule #########################
+	# Switching to a commit letting a submodule appear creates empty dir ...
+	test_expect_success "$command: added submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... and doesn't care if it already exists ...
+	test_expect_success "$command: added submodule leaves existing empty directory alone" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			mkdir sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... unless there is an untracked file in its place.
+	test_expect_success "$command: added submodule does remove untracked unignored file with same name when forced" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			echo -n >sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1
+		)
+	'
+	# Replacing a tracked file with a submodule produces an empty
+	# directory ...
+	test_expect_success "$command: replace tracked file with submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_file &&
+		(
+			cd submodule_update &&
+			git branch -t replace_file_with_sub1 origin/replace_file_with_sub1 &&
+			$command replace_file_with_sub1 &&
+			test_superproject_content origin/replace_file_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_file_with_sub1
+		)
+	'
+	# ... as does removing a directory with tracked files with a
+	# submodule.
+	test_expect_success "$command: replace directory with submodule" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_directory &&
+		(
+			cd submodule_update &&
+			git branch -t replace_directory_with_sub1 origin/replace_directory_with_sub1 &&
+			$command replace_directory_with_sub1 &&
+			test_superproject_content origin/replace_directory_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_directory_with_sub1
+		)
+	'
+
+	######################## Disappearing submodule #######################
+	# Removing a submodule doesn't remove its work tree ...
+	test_expect_success "$command: removed submodule leaves submodule directory and its contents in place" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_success "$command: removed submodule leaves submodule containing a .git directory alone" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			replace_gitfile_with_git_dir sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1
+		)
+	'
+	# Replacing a submodule with files in a directory must fail as the
+	# submodule work tree isn't removed ...
+	test_expect_failure "$command: replace submodule with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_failure "$command: replace submodule containing a .git directory with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1
+		)
+	'
+	# Replacing it with a file must fail as it could throw away any local
+	# work tree changes ...
+	test_expect_failure "$command: replace submodule with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... or even destroy unpushed parts of submodule history if that
+	# still uses a .git directory.
+	test_expect_failure "$command: replace submodule containing a .git directory with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1
+		)
+	'
+
+	########################## Modified submodule #########################
+	# Updating a submodule sha1 doesn't update the submodule's work tree
+	test_expect_success "$command: modified submodule does not update submodule work tree" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t modify_sub1 origin/modify_sub1 &&
+			$command modify_sub1 &&
+			test_superproject_content origin/modify_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			git submodule update &&
+			test_submodule_content sub1 origin/modify_sub1
+		)
+	'
+	# Updating a submodule to an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will fail
+	test_expect_success "$command: modified submodule does not update submodule work tree to invalid commit" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t invalid_sub1 origin/invalid_sub1 &&
+			$command invalid_sub1 &&
+			test_superproject_content origin/invalid_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_must_fail git submodule update &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Updating a submodule from an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will succeed
+	test_expect_success "$command: modified submodule does not update submodule work tree from invalid commit" '
+		prolog &&
+		reset_work_tree_to invalid_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t valid_sub1 origin/valid_sub1 &&
+			$command valid_sub1 &&
+			test_superproject_content origin/valid_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/valid_sub1
+		)
+	'
+}

new file mode 100755
index 0000000..03217b2
@@ -0,0 +1,632 @@
+# Create a submodule layout used for all tests below.
+#
+# The following use cases are covered:
+# - New submodule (no_submodule => add_sub1)
+# - Removed submodule (add_sub1 => remove_sub1)
+# - Updated submodule (add_sub1 => modify_sub1)
+# - Submodule updated to invalid commit (add_sub1 => invalid_sub1)
+# - Submodule updated from invalid commit (invalid_sub1 => valid_sub1)
+# - Submodule replaced by tracked files in directory (add_sub1 =>
+#   replace_sub1_with_directory)
+# - Directory containing tracked files replaced by submodule
+#   (replace_sub1_with_directory => replace_directory_with_sub1)
+# - Submodule replaced by tracked file with the same name (add_sub1 =>
+#   replace_sub1_with_file)
+# - Tracked file replaced by submodule (replace_sub1_with_file =>
+#   replace_file_with_sub1)
+#
+#                   --O-----O
+#                  /  ^     replace_directory_with_sub1
+#                 /   replace_sub1_with_directory
+#                /----O
+#               /     ^
+#              /      modify_sub1
+#      O------O-------O
+#      ^      ^\      ^
+#      |      | \     remove_sub1
+#      |      |  -----O-----O
+#      |      |   \   ^     replace_file_with_sub1
+#      |      |    \  replace_sub1_with_file
+#      |   add_sub1 --O-----O
+# no_submodule        ^     valid_sub1
+#                     invalid_sub1
+#
+create_lib_submodule_repo () {
+	git init submodule_update_repo &&
+	(
+		cd submodule_update_repo &&
+		echo "expect" >>.gitignore &&
+		echo "actual" >>.gitignore &&
+		echo "x" >file1 &&
+		echo "y" >file2 &&
+		git add .gitignore file1 file2 &&
+		git commit -m "Base" &&
+		git branch "no_submodule" &&
+
+		git checkout -b "add_sub1" &&
+		git submodule add ./. sub1 &&
+		git config -f .gitmodules submodule.sub1.ignore all &&
+		git config submodule.sub1.ignore all &&
+		git add .gitmodules &&
+		git commit -m "Add sub1" &&
+		git checkout -b remove_sub1 &&
+		git revert HEAD &&
+
+		git checkout -b "modify_sub1" "add_sub1" &&
+		git submodule update &&
+		(
+			cd sub1 &&
+			git fetch &&
+			git checkout -b "modifications" &&
+			echo "z" >file2 &&
+			echo "x" >file3 &&
+			git add file2 file3 &&
+			git commit -m "modified file2 and added file3" &&
+			git push origin modifications
+		) &&
+		git add sub1 &&
+		git commit -m "Modify sub1" &&
+
+		git checkout -b "replace_sub1_with_directory" "add_sub1" &&
+		git submodule update &&
+		(
+			cd sub1 &&
+			git checkout modifications
+		) &&
+		git rm --cached sub1 &&
+		rm sub1/.git* &&
+		git config -f .gitmodules --remove-section "submodule.sub1" &&
+		git add .gitmodules sub1/* &&
+		git commit -m "Replace sub1 with directory" &&
+		git checkout -b replace_directory_with_sub1 &&
+		git revert HEAD &&
+
+		git checkout -b "replace_sub1_with_file" "add_sub1" &&
+		git rm sub1 &&
+		echo "content" >sub1 &&
+		git add sub1 &&
+		git commit -m "Replace sub1 with file" &&
+		git checkout -b replace_file_with_sub1 &&
+		git revert HEAD &&
+
+		git checkout -b "invalid_sub1" "add_sub1" &&
+		git update-index --cacheinfo 160000 0123456789012345678901234567890123456789 sub1 &&
+		git commit -m "Invalid sub1 commit" &&
+		git checkout -b valid_sub1 &&
+		git revert HEAD &&
+		git checkout master
+	)
+}
+
+# Helper function to replace gitfile with .git directory
+replace_gitfile_with_git_dir () {
+	(
+		cd "$1" &&
+		git_dir="$(git rev-parse --git-dir)" &&
+		rm -f .git &&
+		cp -R "$git_dir" .git &&
+		GIT_WORK_TREE=. git config --unset core.worktree
+	)
+}
+
+# Test that the .git directory in the submodule is unchanged (except for the
+# core.worktree setting, which we temporarily restore). Call this function
+# before test_submodule_content as the latter might write the index file
+# leading to false positive index differences.
+test_git_directory_is_unchanged () {
+	(
+		cd "$1" &&
+		git config core.worktree "../../../$1"
+	) &&
+	diff -r ".git/modules/$1" "$1/.git" &&
+	(
+		cd "$1" &&
+		GIT_WORK_TREE=. git config --unset core.worktree
+	)
+}
+
+# Helper function to be executed at the start of every test below, it sets up
+# the submodule repo if it doesn't exist and configures the most problematic
+# settings for diff.ignoreSubmodules.
+prolog () {
+	(test -d submodule_update_repo || create_lib_submodule_repo) &&
+	test_config_global diff.ignoreSubmodules all &&
+	test_config diff.ignoreSubmodules all
+}
+
+# Helper function to bring work tree back into the state given by the
+# commit. This includes trying to populate sub1 accordingly if it exists and
+# should be updated to an existing commit.
+reset_work_tree_to () {
+	rm -rf submodule_update &&
+	git clone submodule_update_repo submodule_update &&
+	(
+		cd submodule_update &&
+		rm -rf sub1 &&
+		git checkout -f "$1" &&
+		git status -u -s >actual &&
+		test_must_be_empty actual &&
+		sha1=$(git rev-parse HEAD:sub1 || true) &&
+		if test -n "$sha1" &&
+		   test $(cd "sub1" && git rev-parse --verify "$sha1^{commit}")
+		then
+			git submodule update --init --recursive "sub1"
+		fi
+	)
+}
+
+# Test that the superproject contains the content according to commit "$1"
+# (the work tree must match the index for everything but submodules but the
+# index must exactly match the given commit including any submodule SHA-1s).
+test_superproject_content () {
+	git diff-index --cached "$1" >actual &&
+	test_must_be_empty actual &&
+	git diff-files --ignore-submodules >actual &&
+	test_must_be_empty actual
+}
+
+# Test that the given submodule at path "$1" contains the content according
+# to the submodule commit recorded in the superproject's commit "$2"
+test_submodule_content () {
+	if test $# != 2
+	then
+		echo "test_submodule_content needs two arguments"
+		return 1
+	fi &&
+	submodule="$1" &&
+	commit="$2" &&
+	test -d "$submodule"/ &&
+	if ! test -f "$submodule"/.git && ! test -d "$submodule"/.git
+	then
+		echo "Submodule $submodule is not populated"
+		return 1
+	fi &&
+	sha1=$(git rev-parse "$commit:$submodule") &&
+	if test -z "$sha1"
+	then
+		echo "Couldn't retrieve SHA-1 of $submodule for $commit"
+		return 1
+	fi &&
+	(
+		cd "$submodule" &&
+		git status -u -s >actual &&
+		test_must_be_empty actual &&
+		git diff "$sha1" >actual &&
+		test_must_be_empty actual
+	)
+}
+
+# Test that the following transitions are correctly handled:
+# - Updated submodule
+# - New submodule
+# - Removed submodule
+# - Directory containing tracked files replaced by submodule
+# - Submodule replaced by tracked files in directory
+# - Submodule replaced by tracked file with the same name
+# - tracked file replaced by submodule
+#
+# The default is that submodule contents aren't changed until "git submodule
+# update" is run. And even then that command doesn't delete the work tree of
+# a removed submodule.
+#
+# Removing a submodule containing a .git directory must fail even when forced
+# to protect the history!
+#
+
+# Test that submodule contents are currently not updated when switching
+# between commits that change a submodule.
+test_submodule_switch () {
+	command="$1"
+	######################### Appearing submodule #########################
+	# Switching to a commit letting a submodule appear creates empty dir ...
+	test_expect_success "$command: added submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... and doesn't care if it already exists ...
+	test_expect_success "$command: added submodule leaves existing empty directory alone" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			mkdir sub1 &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... unless there is an untracked file in its place.
+	test_expect_success "$command: added submodule doesn't remove untracked unignored file with same name" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			echo -n >sub1 &&
+			test_must_fail $command add_sub1 &&
+			test_superproject_content origin/no_submodule &&
+			test_must_be_empty sub1
+		)
+	'
+	# Replacing a tracked file with a submodule produces an empty
+	# directory ...
+	test_expect_success "$command: replace tracked file with submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_file &&
+		(
+			cd submodule_update &&
+			git branch -t replace_file_with_sub1 origin/replace_file_with_sub1 &&
+			$command replace_file_with_sub1 &&
+			test_superproject_content origin/replace_file_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_file_with_sub1
+		)
+	'
+	# ... as does removing a directory with tracked files with a
+	# submodule.
+	test_expect_success "$command: replace directory with submodule" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_directory &&
+		(
+			cd submodule_update &&
+			git branch -t replace_directory_with_sub1 origin/replace_directory_with_sub1 &&
+			$command replace_directory_with_sub1 &&
+			test_superproject_content origin/replace_directory_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_directory_with_sub1
+		)
+	'
+
+	######################## Disappearing submodule #######################
+	# Removing a submodule doesn't remove its work tree ...
+	test_expect_success "$command: removed submodule leaves submodule directory and its contents in place" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_success "$command: removed submodule leaves submodule containing a .git directory alone" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			replace_gitfile_with_git_dir sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Replacing a submodule with files in a directory must fail as the
+	# submodule work tree isn't removed ...
+	test_expect_success "$command: replace submodule with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_success "$command: replace submodule containing a .git directory with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Replacing it with a file must fail as it could throw away any local
+	# work tree changes ...
+	test_expect_failure "$command: replace submodule with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... or even destroy unpushed parts of submodule history if that
+	# still uses a .git directory.
+	test_expect_failure "$command: replace submodule containing a .git directory with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+
+	########################## Modified submodule #########################
+	# Updating a submodule sha1 doesn't update the submodule's work tree
+	test_expect_success "$command: modified submodule does not update submodule work tree" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t modify_sub1 origin/modify_sub1 &&
+			$command modify_sub1 &&
+			test_superproject_content origin/modify_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			git submodule update &&
+			test_submodule_content sub1 origin/modify_sub1
+		)
+	'
+
+	# Updating a submodule to an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will fail
+	test_expect_success "$command: modified submodule does not update submodule work tree to invalid commit" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t invalid_sub1 origin/invalid_sub1 &&
+			$command invalid_sub1 &&
+			test_superproject_content origin/invalid_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_must_fail git submodule update &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Updating a submodule from an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will succeed
+	test_expect_success "$command: modified submodule does not update submodule work tree from invalid commit" '
+		prolog &&
+		reset_work_tree_to invalid_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t valid_sub1 origin/valid_sub1 &&
+			$command valid_sub1 &&
+			test_superproject_content origin/valid_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/valid_sub1
+		)
+	'
+}
+
+# Test that submodule contents are currently not updated when switching
+# between commits that change a submodule, but throwing away local changes in
+# the superproject is allowed.
+test_submodule_forced_switch () {
+	command="$1"
+	######################### Appearing submodule #########################
+	# Switching to a commit letting a submodule appear creates empty dir ...
+	test_expect_success "$command: added submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... and doesn't care if it already exists ...
+	test_expect_success "$command: added submodule leaves existing empty directory alone" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			mkdir sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... unless there is an untracked file in its place.
+	test_expect_success "$command: added submodule does remove untracked unignored file with same name when forced" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			echo -n >sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1
+		)
+	'
+	# Replacing a tracked file with a submodule produces an empty
+	# directory ...
+	test_expect_success "$command: replace tracked file with submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_file &&
+		(
+			cd submodule_update &&
+			git branch -t replace_file_with_sub1 origin/replace_file_with_sub1 &&
+			$command replace_file_with_sub1 &&
+			test_superproject_content origin/replace_file_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_file_with_sub1
+		)
+	'
+	# ... as does removing a directory with tracked files with a
+	# submodule.
+	test_expect_success "$command: replace directory with submodule" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_directory &&
+		(
+			cd submodule_update &&
+			git branch -t replace_directory_with_sub1 origin/replace_directory_with_sub1 &&
+			$command replace_directory_with_sub1 &&
+			test_superproject_content origin/replace_directory_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_directory_with_sub1
+		)
+	'
+
+	######################## Disappearing submodule #######################
+	# Removing a submodule doesn't remove its work tree ...
+	test_expect_success "$command: removed submodule leaves submodule directory and its contents in place" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_success "$command: removed submodule leaves submodule containing a .git directory alone" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			replace_gitfile_with_git_dir sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Replacing a submodule with files in a directory must fail as the
+	# submodule work tree isn't removed ...
+	test_expect_failure "$command: replace submodule with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_failure "$command: replace submodule containing a .git directory with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Replacing it with a file must fail as it could throw away any local
+	# work tree changes ...
+	test_expect_failure "$command: replace submodule with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... or even destroy unpushed parts of submodule history if that
+	# still uses a .git directory.
+	test_expect_failure "$command: replace submodule containing a .git directory with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+
+	########################## Modified submodule #########################
+	# Updating a submodule sha1 doesn't update the submodule's work tree
+	test_expect_success "$command: modified submodule does not update submodule work tree" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t modify_sub1 origin/modify_sub1 &&
+			$command modify_sub1 &&
+			test_superproject_content origin/modify_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			git submodule update &&
+			test_submodule_content sub1 origin/modify_sub1
+		)
+	'
+	# Updating a submodule to an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will fail
+	test_expect_success "$command: modified submodule does not update submodule work tree to invalid commit" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t invalid_sub1 origin/invalid_sub1 &&
+			$command invalid_sub1 &&
+			test_superproject_content origin/invalid_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_must_fail git submodule update &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Updating a submodule from an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will succeed
+	test_expect_success "$command: modified submodule does not update submodule work tree from invalid commit" '
+		prolog &&
+		reset_work_tree_to invalid_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t valid_sub1 origin/valid_sub1 &&
+			$command valid_sub1 &&
+			test_superproject_content origin/valid_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/valid_sub1
+		)
+	'
+}

new file mode 100755
index 0000000..ceeaaeb
@@ -0,0 +1,632 @@
+# Create a submodule layout used for all tests below.
+#
+# The following use cases are covered:
+# - New submodule (no_submodule => add_sub1)
+# - Removed submodule (add_sub1 => remove_sub1)
+# - Updated submodule (add_sub1 => modify_sub1)
+# - Submodule updated to invalid commit (add_sub1 => invalid_sub1)
+# - Submodule updated from invalid commit (invalid_sub1 => valid_sub1)
+# - Submodule replaced by tracked files in directory (add_sub1 =>
+#   replace_sub1_with_directory)
+# - Directory containing tracked files replaced by submodule
+#   (replace_sub1_with_directory => replace_directory_with_sub1)
+# - Submodule replaced by tracked file with the same name (add_sub1 =>
+#   replace_sub1_with_file)
+# - Tracked file replaced by submodule (replace_sub1_with_file =>
+#   replace_file_with_sub1)
+#
+#                   --O-----O
+#                  /  ^     replace_directory_with_sub1
+#                 /   replace_sub1_with_directory
+#                /----O
+#               /     ^
+#              /      modify_sub1
+#      O------O-------O
+#      ^      ^\      ^
+#      |      | \     remove_sub1
+#      |      |  -----O-----O
+#      |      |   \   ^     replace_file_with_sub1
+#      |      |    \  replace_sub1_with_file
+#      |   add_sub1 --O-----O
+# no_submodule        ^     valid_sub1
+#                     invalid_sub1
+#
+create_lib_submodule_repo () {
+	git init submodule_update_repo &&
+	(
+		cd submodule_update_repo &&
+		echo "expect" >>.gitignore &&
+		echo "actual" >>.gitignore &&
+		echo "x" >file1 &&
+		echo "y" >file2 &&
+		git add .gitignore file1 file2 &&
+		git commit -m "Base" &&
+		git branch "no_submodule" &&
+
+		git checkout -b "add_sub1" &&
+		git submodule add ./. sub1 &&
+		git config -f .gitmodules submodule.sub1.ignore all &&
+		git config submodule.sub1.ignore all &&
+		git add .gitmodules &&
+		git commit -m "Add sub1" &&
+		git checkout -b remove_sub1 &&
+		git revert HEAD &&
+
+		git checkout -b "modify_sub1" "add_sub1" &&
+		git submodule update &&
+		(
+			cd sub1 &&
+			git fetch &&
+			git checkout -b "modifications" &&
+			echo "z" >file2 &&
+			echo "x" >file3 &&
+			git add file2 file3 &&
+			git commit -m "modified file2 and added file3" &&
+			git push origin modifications
+		) &&
+		git add sub1 &&
+		git commit -m "Modify sub1" &&
+
+		git checkout -b "replace_sub1_with_directory" "add_sub1" &&
+		git submodule update &&
+		(
+			cd sub1 &&
+			git checkout modifications
+		) &&
+		git rm --cached sub1 &&
+		rm sub1/.git* &&
+		git config -f .gitmodules --remove-section "submodule.sub1" &&
+		git add .gitmodules sub1/* &&
+		git commit -m "Replace sub1 with directory" &&
+		git checkout -b replace_directory_with_sub1 &&
+		git revert HEAD &&
+
+		git checkout -b "replace_sub1_with_file" "add_sub1" &&
+		git rm sub1 &&
+		echo "content" >sub1 &&
+		git add sub1 &&
+		git commit -m "Replace sub1 with file" &&
+		git checkout -b replace_file_with_sub1 &&
+		git revert HEAD &&
+
+		git checkout -b "invalid_sub1" "add_sub1" &&
+		git update-index --cacheinfo 160000 0123456789012345678901234567890123456789 sub1 &&
+		git commit -m "Invalid sub1 commit" &&
+		git checkout -b valid_sub1 &&
+		git revert HEAD &&
+		git checkout master
+	)
+}
+
+# Helper function to replace gitfile with .git directory
+replace_gitfile_with_git_dir () {
+	(
+		cd "$1" &&
+		git_dir="$(git rev-parse --git-dir)" &&
+		rm -f .git &&
+		cp -R "$git_dir" .git &&
+		GIT_WORK_TREE=. git config --unset core.worktree
+	)
+}
+
+# Test that the .git directory in the submodule is unchanged (except for the
+# core.worktree setting, which we temporarily restore). Call this function
+# before test_submodule_content as the latter might write the index file
+# leading to false positive index differences.
+test_git_directory_is_unchanged () {
+	(
+		cd "$1" &&
+		git config core.worktree "../../../$1"
+	) &&
+	diff -r ".git/modules/$1" "$1/.git" &&
+	(
+		cd "$1" &&
+		GIT_WORK_TREE=. git config --unset core.worktree
+	)
+}
+
+# Helper function to be executed at the start of every test below, it sets up
+# the submodule repo if it doesn't exist and configures the most problematic
+# settings for diff.ignoreSubmodules.
+prolog () {
+	(test -d submodule_update_repo || create_lib_submodule_repo) &&
+	test_config_global diff.ignoreSubmodules all &&
+	test_config diff.ignoreSubmodules all
+}
+
+# Helper function to bring work tree back into the state given by the
+# commit. This includes trying to populate sub1 accordingly if it exists and
+# should be updated to an existing commit.
+reset_work_tree_to () {
+	rm -rf submodule_update &&
+	git clone submodule_update_repo submodule_update &&
+	(
+		cd submodule_update &&
+		rm -rf sub1 &&
+		git checkout -f "$1" &&
+		git status -u -s >actual &&
+		test_must_be_empty actual &&
+		sha1=$(git rev-parse --revs-only HEAD:sub1) &&
+		if test -n "$sha1" &&
+		   test $(cd "sub1" && git rev-parse --verify "$sha1^{commit}")
+		then
+			git submodule update --init --recursive "sub1"
+		fi
+	)
+}
+
+# Test that the superproject contains the content according to commit "$1"
+# (the work tree must match the index for everything but submodules but the
+# index must exactly match the given commit including any submodule SHA-1s).
+test_superproject_content () {
+	git diff-index --cached "$1" >actual &&
+	test_must_be_empty actual &&
+	git diff-files --ignore-submodules >actual &&
+	test_must_be_empty actual
+}
+
+# Test that the given submodule at path "$1" contains the content according
+# to the submodule commit recorded in the superproject's commit "$2"
+test_submodule_content () {
+	if test $# != 2
+	then
+		echo "test_submodule_content needs two arguments"
+		return 1
+	fi &&
+	submodule="$1" &&
+	commit="$2" &&
+	test -d "$submodule"/ &&
+	if ! test -f "$submodule"/.git && ! test -d "$submodule"/.git
+	then
+		echo "Submodule $submodule is not populated"
+		return 1
+	fi &&
+	sha1=$(git rev-parse --verify "$commit:$submodule") &&
+	if test -z "$sha1"
+	then
+		echo "Couldn't retrieve SHA-1 of $submodule for $commit"
+		return 1
+	fi &&
+	(
+		cd "$submodule" &&
+		git status -u -s >actual &&
+		test_must_be_empty actual &&
+		git diff "$sha1" >actual &&
+		test_must_be_empty actual
+	)
+}
+
+# Test that the following transitions are correctly handled:
+# - Updated submodule
+# - New submodule
+# - Removed submodule
+# - Directory containing tracked files replaced by submodule
+# - Submodule replaced by tracked files in directory
+# - Submodule replaced by tracked file with the same name
+# - tracked file replaced by submodule
+#
+# The default is that submodule contents aren't changed until "git submodule
+# update" is run. And even then that command doesn't delete the work tree of
+# a removed submodule.
+#
+# Removing a submodule containing a .git directory must fail even when forced
+# to protect the history!
+#
+
+# Test that submodule contents are currently not updated when switching
+# between commits that change a submodule.
+test_submodule_switch () {
+	command="$1"
+	######################### Appearing submodule #########################
+	# Switching to a commit letting a submodule appear creates empty dir ...
+	test_expect_success "$command: added submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... and doesn't care if it already exists ...
+	test_expect_success "$command: added submodule leaves existing empty directory alone" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			mkdir sub1 &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... unless there is an untracked file in its place.
+	test_expect_success "$command: added submodule doesn't remove untracked unignored file with same name" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			echo -n >sub1 &&
+			test_must_fail $command add_sub1 &&
+			test_superproject_content origin/no_submodule &&
+			test_must_be_empty sub1
+		)
+	'
+	# Replacing a tracked file with a submodule produces an empty
+	# directory ...
+	test_expect_success "$command: replace tracked file with submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_file &&
+		(
+			cd submodule_update &&
+			git branch -t replace_file_with_sub1 origin/replace_file_with_sub1 &&
+			$command replace_file_with_sub1 &&
+			test_superproject_content origin/replace_file_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_file_with_sub1
+		)
+	'
+	# ... as does removing a directory with tracked files with a
+	# submodule.
+	test_expect_success "$command: replace directory with submodule" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_directory &&
+		(
+			cd submodule_update &&
+			git branch -t replace_directory_with_sub1 origin/replace_directory_with_sub1 &&
+			$command replace_directory_with_sub1 &&
+			test_superproject_content origin/replace_directory_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_directory_with_sub1
+		)
+	'
+
+	######################## Disappearing submodule #######################
+	# Removing a submodule doesn't remove its work tree ...
+	test_expect_success "$command: removed submodule leaves submodule directory and its contents in place" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_success "$command: removed submodule leaves submodule containing a .git directory alone" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			replace_gitfile_with_git_dir sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Replacing a submodule with files in a directory must fail as the
+	# submodule work tree isn't removed ...
+	test_expect_success "$command: replace submodule with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_success "$command: replace submodule containing a .git directory with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Replacing it with a file must fail as it could throw away any local
+	# work tree changes ...
+	test_expect_failure "$command: replace submodule with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... or even destroy unpushed parts of submodule history if that
+	# still uses a .git directory.
+	test_expect_failure "$command: replace submodule containing a .git directory with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+
+	########################## Modified submodule #########################
+	# Updating a submodule sha1 doesn't update the submodule's work tree
+	test_expect_success "$command: modified submodule does not update submodule work tree" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t modify_sub1 origin/modify_sub1 &&
+			$command modify_sub1 &&
+			test_superproject_content origin/modify_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			git submodule update &&
+			test_submodule_content sub1 origin/modify_sub1
+		)
+	'
+
+	# Updating a submodule to an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will fail
+	test_expect_success "$command: modified submodule does not update submodule work tree to invalid commit" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t invalid_sub1 origin/invalid_sub1 &&
+			$command invalid_sub1 &&
+			test_superproject_content origin/invalid_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_must_fail git submodule update &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Updating a submodule from an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will succeed
+	test_expect_success "$command: modified submodule does not update submodule work tree from invalid commit" '
+		prolog &&
+		reset_work_tree_to invalid_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t valid_sub1 origin/valid_sub1 &&
+			$command valid_sub1 &&
+			test_superproject_content origin/valid_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/valid_sub1
+		)
+	'
+}
+
+# Test that submodule contents are currently not updated when switching
+# between commits that change a submodule, but throwing away local changes in
+# the superproject is allowed.
+test_submodule_forced_switch () {
+	command="$1"
+	######################### Appearing submodule #########################
+	# Switching to a commit letting a submodule appear creates empty dir ...
+	test_expect_success "$command: added submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... and doesn't care if it already exists ...
+	test_expect_success "$command: added submodule leaves existing empty directory alone" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			mkdir sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... unless there is an untracked file in its place.
+	test_expect_success "$command: added submodule does remove untracked unignored file with same name when forced" '
+		prolog &&
+		reset_work_tree_to no_submodule &&
+		(
+			cd submodule_update &&
+			git branch -t add_sub1 origin/add_sub1 &&
+			echo -n >sub1 &&
+			$command add_sub1 &&
+			test_superproject_content origin/add_sub1 &&
+			test_dir_is_empty sub1
+		)
+	'
+	# Replacing a tracked file with a submodule produces an empty
+	# directory ...
+	test_expect_success "$command: replace tracked file with submodule creates empty directory" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_file &&
+		(
+			cd submodule_update &&
+			git branch -t replace_file_with_sub1 origin/replace_file_with_sub1 &&
+			$command replace_file_with_sub1 &&
+			test_superproject_content origin/replace_file_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_file_with_sub1
+		)
+	'
+	# ... as does removing a directory with tracked files with a
+	# submodule.
+	test_expect_success "$command: replace directory with submodule" '
+		prolog &&
+		reset_work_tree_to replace_sub1_with_directory &&
+		(
+			cd submodule_update &&
+			git branch -t replace_directory_with_sub1 origin/replace_directory_with_sub1 &&
+			$command replace_directory_with_sub1 &&
+			test_superproject_content origin/replace_directory_with_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/replace_directory_with_sub1
+		)
+	'
+
+	######################## Disappearing submodule #######################
+	# Removing a submodule doesn't remove its work tree ...
+	test_expect_success "$command: removed submodule leaves submodule directory and its contents in place" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_success "$command: removed submodule leaves submodule containing a .git directory alone" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t remove_sub1 origin/remove_sub1 &&
+			replace_gitfile_with_git_dir sub1 &&
+			$command remove_sub1 &&
+			test_superproject_content origin/remove_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Replacing a submodule with files in a directory must fail as the
+	# submodule work tree isn't removed ...
+	test_expect_failure "$command: replace submodule with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... especially when it contains a .git directory.
+	test_expect_failure "$command: replace submodule containing a .git directory with a directory must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_directory origin/replace_sub1_with_directory &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_directory &&
+			test_superproject_content origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Replacing it with a file must fail as it could throw away any local
+	# work tree changes ...
+	test_expect_failure "$command: replace submodule with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# ... or even destroy unpushed parts of submodule history if that
+	# still uses a .git directory.
+	test_expect_failure "$command: replace submodule containing a .git directory with a file must fail" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t replace_sub1_with_file origin/replace_sub1_with_file &&
+			replace_gitfile_with_git_dir sub1 &&
+			test_must_fail $command replace_sub1_with_file &&
+			test_superproject_content origin/add_sub1 &&
+			test_git_directory_is_unchanged sub1 &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+
+	########################## Modified submodule #########################
+	# Updating a submodule sha1 doesn't update the submodule's work tree
+	test_expect_success "$command: modified submodule does not update submodule work tree" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t modify_sub1 origin/modify_sub1 &&
+			$command modify_sub1 &&
+			test_superproject_content origin/modify_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			git submodule update &&
+			test_submodule_content sub1 origin/modify_sub1
+		)
+	'
+	# Updating a submodule to an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will fail
+	test_expect_success "$command: modified submodule does not update submodule work tree to invalid commit" '
+		prolog &&
+		reset_work_tree_to add_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t invalid_sub1 origin/invalid_sub1 &&
+			$command invalid_sub1 &&
+			test_superproject_content origin/invalid_sub1 &&
+			test_submodule_content sub1 origin/add_sub1 &&
+			test_must_fail git submodule update &&
+			test_submodule_content sub1 origin/add_sub1
+		)
+	'
+	# Updating a submodule from an invalid sha1 doesn't update the
+	# submodule's work tree, subsequent update will succeed
+	test_expect_success "$command: modified submodule does not update submodule work tree from invalid commit" '
+		prolog &&
+		reset_work_tree_to invalid_sub1 &&
+		(
+			cd submodule_update &&
+			git branch -t valid_sub1 origin/valid_sub1 &&
+			$command valid_sub1 &&
+			test_superproject_content origin/valid_sub1 &&
+			test_dir_is_empty sub1 &&
+			git submodule update --init --recursive &&
+			test_submodule_content sub1 origin/valid_sub1
+		)
+	'
+}

index 06b18f8..6847f75 100755
@@ -3,6 +3,7 @@
 test_description='checkout can handle submodules'
 
 . ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
 
 test_expect_success 'setup' '
 	mkdir submodule &&

@@ -62,4 +63,8 @@ test_expect_success '"checkout <submodule>" honors submodule.*.ignore from .git/
 	! test -s actual
 '
 
+test_submodule_switch "git checkout"
+
+test_submodule_forced_switch "git checkout -f"
+
 test_done

new file mode 100755
index 0000000..a9bd40a
@@ -0,0 +1,20 @@
+#!/bin/sh
+
+test_description='git apply handling submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+apply_index () {
+	git diff --ignore-submodules=dirty "..$1" | git apply --index -
+}
+
+test_submodule_switch "apply_index"
+
+apply_3way () {
+	git diff --ignore-submodules=dirty "..$1" | git apply --3way -
+}
+
+test_submodule_switch "apply_3way"
+
+test_done

new file mode 100755
index 0000000..20526ae
@@ -0,0 +1,12 @@
+#!/bin/sh
+
+test_description='read-tree can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+test_submodule_switch "git read-tree -u -m"
+
+test_submodule_forced_switch "git read-tree -u --reset"
+
+test_done

new file mode 100755
index 0000000..2eda6ad
@@ -0,0 +1,14 @@
+#!/bin/sh
+
+test_description='reset can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+test_submodule_switch "git reset --keep"
+
+test_submodule_switch "git reset --merge"
+
+test_submodule_forced_switch "git reset --hard"
+
+test_done

new file mode 100755
index 0000000..4f37d24
@@ -0,0 +1,32 @@
+#!/bin/sh
+
+test_description='bisect can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+git_bisect () {
+	git status -su >expected &&
+	ls -1pR * >>expected &&
+	tar czf "$TRASH_DIRECTORY/tmp.tgz" * &&
+	GOOD=$(git rev-parse --verify HEAD) &&
+	git checkout "$1" &&
+	echo "foo" >bar &&
+	git add bar &&
+	git commit -m "bisect bad" &&
+	BAD=$(git rev-parse --verify HEAD) &&
+	git reset --hard HEAD^^ &&
+	git submodule update &&
+	git bisect start &&
+	git bisect good $GOOD &&
+	rm -rf * &&
+	tar xzf "$TRASH_DIRECTORY/tmp.tgz" &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expected actual &&
+	git bisect bad $BAD
+}
+
+test_submodule_switch "git_bisect"
+
+test_done

new file mode 100755
index 0000000..c6b7aa6
@@ -0,0 +1,32 @@
+#!/bin/sh
+
+test_description='bisect can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+git_bisect () {
+	git status -su >expect &&
+	ls -1pR * >>expect &&
+	tar czf "$TRASH_DIRECTORY/tmp.tgz" * &&
+	GOOD=$(git rev-parse --verify HEAD) &&
+	git checkout "$1" &&
+	echo "foo" >bar &&
+	git add bar &&
+	git commit -m "bisect bad" &&
+	BAD=$(git rev-parse --verify HEAD) &&
+	git reset --hard HEAD^^ &&
+	git submodule update &&
+	git bisect start &&
+	git bisect good $GOOD &&
+	rm -rf * &&
+	tar xzf "$TRASH_DIRECTORY/tmp.tgz" &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expect actual &&
+	git bisect bad $BAD
+}
+
+test_submodule_switch "git_bisect"
+
+test_done

index c6c842a..bc9415c 100755
@@ -275,7 +275,16 @@ test_submodule_switch () {
 	'
 	# ... as does removing a directory with tracked files with a
 	# submodule.
-	test_expect_success "$command: replace directory with submodule" '
+	if test "$KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR" = 1
+	then
+		# Non fast-forward merges fail with "Directory sub1 doesn't
+		# exist. sub1" because the empty submodule directory is not
+		# created
+		RESULT="failure"
+	else
+		RESULT="success"
+	fi
+	test_expect_$RESULT "$command: replace directory with submodule" '
 		prolog &&
 		reset_work_tree_to replace_sub1_with_directory &&
 		(

@@ -318,7 +327,16 @@ test_submodule_switch () {
 	'
 	# Replacing a submodule with files in a directory must fail as the
 	# submodule work tree isn't removed ...
-	test_expect_success "$command: replace submodule with a directory must fail" '
+	if test "$KNOWN_FAILURE_NOFF_MERGE_ATTEMPTS_TO_MERGE_REMOVED_SUBMODULE_FILES" = 1
+	then
+		# Non fast-forward merges attempt to merge the former
+		# submodule files with the newly checked out ones in the
+		# directory of the same name while it shouldn't.
+		RESULT="failure"
+	else
+		RESULT="success"
+	fi
+	test_expect_$RESULT "$command: replace submodule with a directory must fail" '
 		prolog &&
 		reset_work_tree_to add_sub1 &&
 		(

@@ -330,7 +348,7 @@ test_submodule_switch () {
 		)
 	'
 	# ... especially when it contains a .git directory.
-	test_expect_success "$command: replace submodule containing a .git directory with a directory must fail" '
+	test_expect_$RESULT "$command: replace submodule containing a .git directory with a directory must fail" '
 		prolog &&
 		reset_work_tree_to add_sub1 &&
 		(

new file mode 100755
index 0000000..d1e9fcc
@@ -0,0 +1,19 @@
+#!/bin/sh
+
+test_description='merge can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+# merges without conflicts
+test_submodule_switch "git merge"
+
+test_submodule_switch "git merge --ff"
+
+test_submodule_switch "git merge --ff-only"
+
+KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR=1
+KNOWN_FAILURE_NOFF_MERGE_ATTEMPTS_TO_MERGE_REMOVED_SUBMODULE_FILES=1
+test_submodule_switch "git merge --no-ff"
+
+test_done

new file mode 100755
index 0000000..019ce52
@@ -0,0 +1,46 @@
+#!/bin/sh
+
+test_description='rebase can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+. "$TEST_DIRECTORY"/lib-rebase.sh
+
+git_rebase () {
+	git status -su >expected &&
+	ls -1pR * >>expected &&
+	git checkout -b ours HEAD &&
+	echo x >>file1 &&
+	git add file1 &&
+	git commit -m add_x &&
+	git revert HEAD &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expected actual &&
+	git rebase "$1"
+}
+
+test_submodule_switch "git_rebase"
+
+git_rebase_interactive () {
+	git status -su >expected &&
+	ls -1pR * >>expected &&
+	git checkout -b ours HEAD &&
+	echo x >>file1 &&
+	git add file1 &&
+	git commit -m add_x &&
+	git revert HEAD &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expected actual &&
+	set_fake_editor &&
+	echo "fake-editor.sh" >.git/info/exclude
+	git rebase -i "$1"
+}
+
+KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR=1
+# The real reason "replace directory with submodule" fails is because a
+# directory "sub1" exists, but we reuse the suppression added for merge here
+test_submodule_switch "git_rebase_interactive"
+
+test_done

new file mode 100755
index 0000000..d5b896d
@@ -0,0 +1,46 @@
+#!/bin/sh
+
+test_description='rebase can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+. "$TEST_DIRECTORY"/lib-rebase.sh
+
+git_rebase () {
+	git status -su >expect &&
+	ls -1pR * >>expect &&
+	git checkout -b ours HEAD &&
+	echo x >>file1 &&
+	git add file1 &&
+	git commit -m add_x &&
+	git revert HEAD &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expect actual &&
+	git rebase "$1"
+}
+
+test_submodule_switch "git_rebase"
+
+git_rebase_interactive () {
+	git status -su >expect &&
+	ls -1pR * >>expect &&
+	git checkout -b ours HEAD &&
+	echo x >>file1 &&
+	git add file1 &&
+	git commit -m add_x &&
+	git revert HEAD &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expect actual &&
+	set_fake_editor &&
+	echo "fake-editor.sh" >.git/info/exclude &&
+	git rebase -i "$1"
+}
+
+KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR=1
+# The real reason "replace directory with submodule" fails is because a
+# directory "sub1" exists, but we reuse the suppression added for merge here
+test_submodule_switch "git_rebase_interactive"
+
+test_done

new file mode 100755
index 0000000..accfa5c
@@ -0,0 +1,45 @@
+#!/bin/sh
+
+test_description='pull can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+reset_branch_to_HEAD () {
+	git branch -D "$1" &&
+	git checkout -b "$1" HEAD &&
+	git branch --set-upstream-to="origin/$1" "$1"
+}
+
+git_pull () {
+	reset_branch_to_HEAD "$1" &&
+	git pull
+}
+
+# pulls without conflicts
+test_submodule_switch "git_pull"
+
+git_pull_ff () {
+	reset_branch_to_HEAD "$1" &&
+	git pull --ff
+}
+
+test_submodule_switch "git_pull_ff"
+
+git_pull_ff_only () {
+	reset_branch_to_HEAD "$1" &&
+	git pull --ff-only
+}
+
+test_submodule_switch "git_pull_ff_only"
+
+git_pull_noff () {
+	reset_branch_to_HEAD "$1" &&
+	git pull --no-ff
+}
+
+KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR=1
+KNOWN_FAILURE_NOFF_MERGE_ATTEMPTS_TO_MERGE_REMOVED_SUBMODULE_FILES=1
+test_submodule_switch "git_pull_noff"
+
+test_done

index bc9415c..95e041b 100755
@@ -392,7 +392,16 @@ test_submodule_switch () {
 
 	########################## Modified submodule #########################
 	# Updating a submodule sha1 doesn't update the submodule's work tree
-	test_expect_success "$command: modified submodule does not update submodule work tree" '
+	if test "$KNOWN_FAILURE_CHERRY_PICK_SEES_EMPTY_COMMIT" = 1
+	then
+		# When cherry picking a SHA-1 update for an ignored submodule
+		# the commit incorrectly fails with "The previous cherry-pick
+		# is now empty, possibly due to conflict resolution."
+		RESULT="failure"
+	else
+		RESULT="success"
+	fi
+	test_expect_$RESULT "$command: modified submodule does not update submodule work tree" '
 		prolog &&
 		reset_work_tree_to add_sub1 &&
 		(

@@ -408,7 +417,7 @@ test_submodule_switch () {
 
 	# Updating a submodule to an invalid sha1 doesn't update the
 	# submodule's work tree, subsequent update will fail
-	test_expect_success "$command: modified submodule does not update submodule work tree to invalid commit" '
+	test_expect_$RESULT "$command: modified submodule does not update submodule work tree to invalid commit" '
 		prolog &&
 		reset_work_tree_to add_sub1 &&
 		(

@@ -423,7 +432,7 @@ test_submodule_switch () {
 	'
 	# Updating a submodule from an invalid sha1 doesn't update the
 	# submodule's work tree, subsequent update will succeed
-	test_expect_success "$command: modified submodule does not update submodule work tree from invalid commit" '
+	test_expect_$RESULT "$command: modified submodule does not update submodule work tree from invalid commit" '
 		prolog &&
 		reset_work_tree_to invalid_sub1 &&
 		(

new file mode 100755
index 0000000..6863b7b
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+test_description='cherry-pick can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+KNOWN_FAILURE_CHERRY_PICK_SEES_EMPTY_COMMIT=1
+KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR=1
+KNOWN_FAILURE_NOFF_MERGE_ATTEMPTS_TO_MERGE_REMOVED_SUBMODULE_FILES=1
+test_submodule_switch "git cherry-pick"
+
+test_done

new file mode 100755
index 0000000..8bde7db
@@ -0,0 +1,21 @@
+#!/bin/sh
+
+test_description='git am handling submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+am () {
+	git format-patch --stdout --ignore-submodules=dirty "..$1" | git am -
+}
+
+test_submodule_switch "am"
+
+am_3way () {
+	git format-patch --stdout --ignore-submodules=dirty "..$1" | git am --3way -
+}
+
+KNOWN_FAILURE_NOFF_MERGE_ATTEMPTS_TO_MERGE_REMOVED_SUBMODULE_FILES=1
+test_submodule_switch "am_3way"
+
+test_done

index 95e041b..9901b45 100755
@@ -217,7 +217,14 @@ test_submodule_switch () {
 	command="$1"
 	######################### Appearing submodule #########################
 	# Switching to a commit letting a submodule appear creates empty dir ...
-	test_expect_success "$command: added submodule creates empty directory" '
+	if test "$KNOWN_FAILURE_STASH_DOES_IGNORE_SUBMODULE_CHANGES" = 1
+	then
+		# Restoring stash fails to restore submodule index entry
+		RESULT="failure"
+	else
+		RESULT="success"
+	fi
+	test_expect_$RESULT "$command: added submodule creates empty directory" '
 		prolog &&
 		reset_work_tree_to no_submodule &&
 		(

@@ -231,7 +238,7 @@ test_submodule_switch () {
 		)
 	'
 	# ... and doesn't care if it already exists ...
-	test_expect_success "$command: added submodule leaves existing empty directory alone" '
+	test_expect_$RESULT "$command: added submodule leaves existing empty directory alone" '
 		prolog &&
 		reset_work_tree_to no_submodule &&
 		(

@@ -260,7 +267,7 @@ test_submodule_switch () {
 	'
 	# Replacing a tracked file with a submodule produces an empty
 	# directory ...
-	test_expect_success "$command: replace tracked file with submodule creates empty directory" '
+	test_expect_$RESULT "$command: replace tracked file with submodule creates empty directory" '
 		prolog &&
 		reset_work_tree_to replace_sub1_with_file &&
 		(

@@ -300,7 +307,13 @@ test_submodule_switch () {
 
 	######################## Disappearing submodule #######################
 	# Removing a submodule doesn't remove its work tree ...
-	test_expect_success "$command: removed submodule leaves submodule directory and its contents in place" '
+	if test "$KNOWN_FAILURE_STASH_DOES_IGNORE_SUBMODULE_CHANGES" = 1
+	then
+		RESULT="failure"
+	else
+		RESULT="success"
+	fi
+	test_expect_$RESULT "$command: removed submodule leaves submodule directory and its contents in place" '
 		prolog &&
 		reset_work_tree_to add_sub1 &&
 		(

@@ -312,7 +325,7 @@ test_submodule_switch () {
 		)
 	'
 	# ... especially when it contains a .git directory.
-	test_expect_success "$command: removed submodule leaves submodule containing a .git directory alone" '
+	test_expect_$RESULT "$command: removed submodule leaves submodule containing a .git directory alone" '
 		prolog &&
 		reset_work_tree_to add_sub1 &&
 		(

new file mode 100755
index 0000000..aaee424
@@ -0,0 +1,24 @@
+#!/bin/sh
+
+test_description='stash apply can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+git_stash () {
+	git status -su >expected &&
+	ls -1pR * >>expected &&
+	git read-tree -u -m "$1" &&
+	git stash &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expected actual &&
+	git stash apply
+}
+
+KNOWN_FAILURE_STASH_DOES_IGNORE_SUBMODULE_CHANGES=1
+KNOWN_FAILURE_CHERRY_PICK_SEES_EMPTY_COMMIT=1
+KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR=1
+test_submodule_switch "git_stash"
+
+test_done

index a38cf52..2a504b2 100755
@@ -219,7 +219,14 @@ test_submodule_switch () {
 	command="$1"
 	######################### Appearing submodule #########################
 	# Switching to a commit letting a submodule appear creates empty dir ...
-	test_expect_success "$command: added submodule creates empty directory" '
+	if test "$KNOWN_FAILURE_STASH_DOES_IGNORE_SUBMODULE_CHANGES" = 1
+	then
+		# Restoring stash fails to restore submodule index entry
+		RESULT="failure"
+	else
+		RESULT="success"
+	fi
+	test_expect_$RESULT "$command: added submodule creates empty directory" '
 		prolog &&
 		reset_work_tree_to no_submodule &&
 		(

@@ -233,7 +240,7 @@ test_submodule_switch () {
 		)
 	'
 	# ... and doesn't care if it already exists ...
-	test_expect_success "$command: added submodule leaves existing empty directory alone" '
+	test_expect_$RESULT "$command: added submodule leaves existing empty directory alone" '
 		prolog &&
 		reset_work_tree_to no_submodule &&
 		(

@@ -262,7 +269,7 @@ test_submodule_switch () {
 	'
 	# Replacing a tracked file with a submodule produces an empty
 	# directory ...
-	test_expect_success "$command: replace tracked file with submodule creates empty directory" '
+	test_expect_$RESULT "$command: replace tracked file with submodule creates empty directory" '
 		prolog &&
 		reset_work_tree_to replace_sub1_with_file &&
 		(

@@ -302,7 +309,13 @@ test_submodule_switch () {
 
 	######################## Disappearing submodule #######################
 	# Removing a submodule doesn't remove its work tree ...
-	test_expect_success "$command: removed submodule leaves submodule directory and its contents in place" '
+	if test "$KNOWN_FAILURE_STASH_DOES_IGNORE_SUBMODULE_CHANGES" = 1
+	then
+		RESULT="failure"
+	else
+		RESULT="success"
+	fi
+	test_expect_$RESULT "$command: removed submodule leaves submodule directory and its contents in place" '
 		prolog &&
 		reset_work_tree_to add_sub1 &&
 		(

@@ -314,7 +327,7 @@ test_submodule_switch () {
 		)
 	'
 	# ... especially when it contains a .git directory.
-	test_expect_success "$command: removed submodule leaves submodule containing a .git directory alone" '
+	test_expect_$RESULT "$command: removed submodule leaves submodule containing a .git directory alone" '
 		prolog &&
 		reset_work_tree_to add_sub1 &&
 		(

new file mode 100755
index 0000000..d7219d6
@@ -0,0 +1,24 @@
+#!/bin/sh
+
+test_description='stash apply can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+git_stash () {
+	git status -su >expect &&
+	ls -1pR * >>expect &&
+	git read-tree -u -m "$1" &&
+	git stash &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expect actual &&
+	git stash apply
+}
+
+KNOWN_FAILURE_STASH_DOES_IGNORE_SUBMODULE_CHANGES=1
+KNOWN_FAILURE_CHERRY_PICK_SEES_EMPTY_COMMIT=1
+KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR=1
+test_submodule_switch "git_stash"
+
+test_done

new file mode 100755
index 0000000..57e2d75
@@ -0,0 +1,32 @@
+#!/bin/sh
+
+test_description='revert can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+# Create a revert that moves from HEAD (including any test modifications to
+# the work tree) to $1 by first checking out $1 and reverting it. Reverting
+# the revert is the transition we test for. We tar the current work tree
+# first so we can restore the work tree test setup after doing the checkout
+# and revert.  We test here that the restored work tree content is identical
+# to that at the beginning. The last revert is then tested by the framework.
+git_revert () {
+	git status -su >expected &&
+	ls -1pR * >>expected &&
+	tar czf "$TRASH_DIRECTORY/tmp.tgz" * &&
+	git checkout "$1" &&
+	git revert HEAD &&
+	rm -rf * &&
+	tar xzf "$TRASH_DIRECTORY/tmp.tgz" &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expected actual &&
+	git revert HEAD
+}
+
+KNOWN_FAILURE_CHERRY_PICK_SEES_EMPTY_COMMIT=1
+KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR=1
+test_submodule_switch "git_revert"
+
+test_done

new file mode 100755
index 0000000..a1c4e02
@@ -0,0 +1,32 @@
+#!/bin/sh
+
+test_description='revert can handle submodules'
+
+. ./test-lib.sh
+. "$TEST_DIRECTORY"/lib-submodule-update.sh
+
+# Create a revert that moves from HEAD (including any test modifications to
+# the work tree) to $1 by first checking out $1 and reverting it. Reverting
+# the revert is the transition we test for. We tar the current work tree
+# first so we can restore the work tree test setup after doing the checkout
+# and revert.  We test here that the restored work tree content is identical
+# to that at the beginning. The last revert is then tested by the framework.
+git_revert () {
+	git status -su >expect &&
+	ls -1pR * >>expect &&
+	tar czf "$TRASH_DIRECTORY/tmp.tgz" * &&
+	git checkout "$1" &&
+	git revert HEAD &&
+	rm -rf * &&
+	tar xzf "$TRASH_DIRECTORY/tmp.tgz" &&
+	git status -su >actual &&
+	ls -1pR * >>actual &&
+	test_cmp expect actual &&
+	git revert HEAD
+}
+
+KNOWN_FAILURE_CHERRY_PICK_SEES_EMPTY_COMMIT=1
+KNOWN_FAILURE_NOFF_MERGE_DOESNT_CREATE_EMPTY_SUBMODULE_DIR=1
+test_submodule_switch "git_revert"
+
+test_done

index 24c9fd7..3584755 100755
@@ -304,7 +304,7 @@ test_submodule_switch () {
 		(
 			cd submodule_update &&
 			git branch -t add_sub1 origin/add_sub1 &&
-			echo -n >sub1 &&
+			>sub1 &&
 			test_must_fail $command add_sub1 &&
 			test_superproject_content origin/no_submodule &&
 			test_must_be_empty sub1

@@ -547,7 +547,7 @@ test_submodule_forced_switch () {
 		(
 			cd submodule_update &&
 			git branch -t add_sub1 origin/add_sub1 &&
-			echo -n >sub1 &&
+			>sub1 &&
 			$command add_sub1 &&
 			test_superproject_content origin/add_sub1 &&
 			test_dir_is_empty sub1

index 24c9fd7..3584755 100755
@@ -304,7 +304,7 @@ test_submodule_switch () {
 		(
 			cd submodule_update &&
 			git branch -t add_sub1 origin/add_sub1 &&
-			echo -n >sub1 &&
+			>sub1 &&
 			test_must_fail $command add_sub1 &&
 			test_superproject_content origin/no_submodule &&
 			test_must_be_empty sub1

@@ -547,7 +547,7 @@ test_submodule_forced_switch () {
 		(
 			cd submodule_update &&
 			git branch -t add_sub1 origin/add_sub1 &&
-			echo -n >sub1 &&
+			>sub1 &&
 			$command add_sub1 &&
 			test_superproject_content origin/add_sub1 &&
 			test_dir_is_empty sub1

index 3584755..98c86e3 100755
@@ -143,18 +143,18 @@ replace_gitfile_with_git_dir () {
 }
 
 # Test that the .git directory in the submodule is unchanged (except for the
-# core.worktree setting, which we temporarily restore). Call this function
+# core.worktree setting, which we temporarily remove). Call this function
 # before test_submodule_content as the latter might write the index file
 # leading to false positive index differences.
 test_git_directory_is_unchanged () {
 	(
-		cd "$1" &&
-		git config core.worktree "../../../$1"
+		cd ".git/modules/$1" &&
+		git config --unset core.worktree
 	) &&
 	diff -r ".git/modules/$1" "$1/.git" &&
 	(
-		cd "$1" &&
-		GIT_WORK_TREE=. git config --unset core.worktree
+		cd ".git/modules/$1" &&
+		git config core.worktree "../../../$1"
 	)
 }

index e441b98..fc1da84 100755
@@ -110,18 +110,23 @@ replace_gitfile_with_git_dir () {
 }
 
 # Test that the .git directory in the submodule is unchanged (except for the
-# core.worktree setting, which we temporarily restore). Call this function
-# before test_submodule_content as the latter might write the index file
-# leading to false positive index differences.
+# core.worktree setting, which appears only in $GIT_DIR/modules/$1/config).
+# Call this function before test_submodule_content as the latter might
+# write the index file leading to false positive index differences.
 test_git_directory_is_unchanged () {
 	(
-		cd "$1" &&
-		git config core.worktree "../../../$1"
+		cd ".git/modules/$1" &&
+		# does core.worktree point at the right place?
+		test "$(git config core.worktree)" = "../../../$1" &&
+		# remove it temporarily before comparing, as
+		# "$1/.git/config" lacks it...
+		git config --unset core.worktree
 	) &&
 	diff -r ".git/modules/$1" "$1/.git" &&
 	(
-		cd "$1" &&
-		GIT_WORK_TREE=. git config --unset core.worktree
+		# ... and then restore.
+		cd ".git/modules/$1" &&
+		git config core.worktree "../../../$1"
 	)
 }