diff --git a/Documentation/git-rev-parse.txt b/Documentation/git-rev-parse.txt
index 42c9676eaa..8023dc086d 100644
--- a/Documentation/git-rev-parse.txt
+++ b/Documentation/git-rev-parse.txt
@@ -180,6 +180,10 @@ print a message to stderr and exit with nonzero status.
 <args>...::
 	Flags and parameters to be parsed.
 
+--resolve-git-dir <path>::
+	Check if <path> is a valid git-dir or a git-file pointing to a valid
+	git-dir. If <path> is a valid git-dir the resolved path to git-dir will
+	be printed.
 
 include::revisions.txt[]
 
diff --git a/builtin/rev-parse.c b/builtin/rev-parse.c
index 4c19f844a9..98d1cbecca 100644
--- a/builtin/rev-parse.c
+++ b/builtin/rev-parse.c
@@ -468,6 +468,14 @@ int cmd_rev_parse(int argc, const char **argv, const char *prefix)
 		return 0;
 	}
 
+	if (argc > 2 && !strcmp(argv[1], "--resolve-git-dir")) {
+		const char *gitdir = resolve_gitdir(argv[2]);
+		if (!gitdir)
+			die("not a gitdir '%s'", argv[2]);
+		puts(gitdir);
+		return 0;
+	}
+
 	if (argc > 1 && !strcmp("-h", argv[1]))
 		usage(builtin_rev_parse_usage);
 
diff --git a/cache.h b/cache.h
index 82e12c862c..c989f79835 100644
--- a/cache.h
+++ b/cache.h
@@ -439,6 +439,7 @@ extern const char *get_git_namespace(void);
 extern const char *strip_namespace(const char *namespaced_ref);
 extern const char *get_git_work_tree(void);
 extern const char *read_gitfile(const char *path);
+extern const char *resolve_gitdir(const char *suspect);
 extern void set_git_work_tree(const char *tree);
 
 #define ALTERNATE_DB_ENVIRONMENT "GIT_ALTERNATE_OBJECT_DIRECTORIES"
diff --git a/git-submodule.sh b/git-submodule.sh
index 814d0d914e..928a62f626 100755
--- a/git-submodule.sh
+++ b/git-submodule.sh
@@ -128,13 +128,49 @@ module_clone()
 		quiet=-q
 	fi
 
-	if test -n "$reference"
+	gitdir=
+	gitdir_base=
+	name=$(module_name "$path")
+	base_path=$(dirname "$path")
+
+	gitdir=$(git rev-parse --git-dir)
+	gitdir_base="$gitdir/modules/$base_path"
+	gitdir="$gitdir/modules/$path"
+
+	case $gitdir in
+	/*)
+		a="$(cd_to_toplevel && pwd)/"
+		b=$gitdir
+		while [ "$b" ] && [ "${a%%/*}" = "${b%%/*}" ]
+		do
+			a=${a#*/} b=${b#*/};
+		done
+
+		rel="$a$name"
+		rel=`echo $rel | sed -e 's|[^/]*|..|g'`
+		rel_gitdir="$rel/$b"
+		;;
+	*)
+		rel=`echo $name | sed -e 's|[^/]*|..|g'`
+		rel_gitdir="$rel/$gitdir"
+		;;
+	esac
+
+	if test -d "$gitdir"
 	then
-		git-clone $quiet "$reference" -n "$url" "$path"
+		mkdir -p "$path"
+		echo "gitdir: $rel_gitdir" >"$path/.git"
+		rm -f "$gitdir/index"
 	else
-		git-clone $quiet -n "$url" "$path"
-	fi ||
-	die "$(eval_gettext "Clone of '\$url' into submodule path '\$path' failed")"
+		mkdir -p "$gitdir_base"
+		if test -n "$reference"
+		then
+			git-clone $quiet "$reference" -n "$url" "$path" --separate-git-dir "$gitdir"
+		else
+			git-clone $quiet -n "$url" "$path" --separate-git-dir "$gitdir"
+		fi ||
+		die "$(eval_gettext "Clone of '\$url' into submodule path '\$path' failed")"
+	fi
 }
 
 #
@@ -426,6 +462,9 @@ cmd_update()
 		--recursive)
 			recursive=1
 			;;
+		--checkout)
+			update="checkout"
+			;;
 		--)
 			shift
 			break
@@ -458,7 +497,19 @@ cmd_update()
 		fi
 		name=$(module_name "$path") || exit
 		url=$(git config submodule."$name".url)
-		update_module=$(git config submodule."$name".update)
+		if ! test -z "$update"
+		then
+			update_module=$update
+		else
+			update_module=$(git config submodule."$name".update)
+		fi
+
+		if test "$update_module" = "none"
+		then
+			echo "Skipping submodule '$path'"
+			continue
+		fi
+
 		if test -z "$url"
 		then
 			# Only mention uninitialized submodules when its
@@ -480,11 +531,6 @@ Maybe you want to use 'update --init'?")"
 			die "$(eval_gettext "Unable to find current revision in submodule path '\$path'")"
 		fi
 
-		if ! test -z "$update"
-		then
-			update_module=$update
-		fi
-
 		if test "$subsha1" != "$sha1"
 		then
 			subforce=$force
diff --git a/setup.c b/setup.c
index 27c1d4787a..b2b4872b70 100644
--- a/setup.c
+++ b/setup.c
@@ -812,3 +812,10 @@ const char *setup_git_directory(void)
 {
 	return setup_git_directory_gently(NULL);
 }
+
+const char *resolve_gitdir(const char *suspect)
+{
+	if (is_git_directory(suspect))
+		return suspect;
+	return read_gitfile(suspect);
+}
diff --git a/t/t7400-submodule-basic.sh b/t/t7400-submodule-basic.sh
index 69115269c2..695f7afdf3 100755
--- a/t/t7400-submodule-basic.sh
+++ b/t/t7400-submodule-basic.sh
@@ -362,10 +362,10 @@ test_expect_success 'update --init' '
 	git submodule update init > update.out &&
 	cat update.out &&
 	test_i18ngrep "not initialized" update.out &&
-	! test -d init/.git &&
+	test_must_fail git rev-parse --resolve-git-dir init/.git &&
 
 	git submodule update --init init &&
-	test -d init/.git
+	git rev-parse --resolve-git-dir init/.git
 '
 
 test_expect_success 'do not add files from a submodule' '
diff --git a/t/t7403-submodule-sync.sh b/t/t7403-submodule-sync.sh
index 95ffe349a7..3620215c1f 100755
--- a/t/t7403-submodule-sync.sh
+++ b/t/t7403-submodule-sync.sh
@@ -56,8 +56,9 @@ test_expect_success '"git submodule sync" should update submodule URLs' '
 	 git pull --no-recurse-submodules &&
 	 git submodule sync
 	) &&
-	test -d "$(git config -f super-clone/submodule/.git/config \
-	                        remote.origin.url)" &&
+	test -d "$(cd super-clone/submodule &&
+	 git config remote.origin.url
+	)" &&
 	(cd super-clone/submodule &&
 	 git checkout master &&
 	 git pull
diff --git a/t/t7406-submodule-update.sh b/t/t7406-submodule-update.sh
index c679f36a4d..1ae6b4e936 100755
--- a/t/t7406-submodule-update.sh
+++ b/t/t7406-submodule-update.sh
@@ -408,6 +408,7 @@ test_expect_success 'submodule update exit immediately in case of merge conflict
 	 test_cmp expect actual
 	)
 '
+
 test_expect_success 'submodule update exit immediately after recursive rebase error' '
 	(cd super &&
 	 git checkout master &&
@@ -442,4 +443,110 @@ test_expect_success 'submodule update exit immediately after recursive rebase er
 	 test_cmp expect actual
 	)
 '
+
+test_expect_success 'add different submodules to the same path' '
+	(cd super &&
+	 git submodule add ../submodule s1 &&
+	 test_must_fail git submodule add ../merging s1
+	)
+'
+
+test_expect_success 'submodule add places git-dir in superprojects git-dir' '
+	(cd super &&
+	 mkdir deeper &&
+	 git submodule add ../submodule deeper/submodule &&
+	 (cd deeper/submodule &&
+	  git log > ../../expected
+	 ) &&
+	 (cd .git/modules/deeper/submodule &&
+	  git log > ../../../../actual
+	 ) &&
+	 test_cmp actual expected
+	)
+'
+
+test_expect_success 'submodule update places git-dir in superprojects git-dir' '
+	(cd super &&
+	 git commit -m "added submodule"
+	) &&
+	git clone super super2 &&
+	(cd super2 &&
+	 git submodule init deeper/submodule &&
+	 git submodule update &&
+	 (cd deeper/submodule &&
+	  git log > ../../expected
+	 ) &&
+	 (cd .git/modules/deeper/submodule &&
+	  git log > ../../../../actual
+	 ) &&
+	 test_cmp actual expected
+	)
+'
+
+test_expect_success 'submodule add places git-dir in superprojects git-dir recursive' '
+	(cd super2 &&
+	 (cd deeper/submodule &&
+	  git submodule add ../submodule subsubmodule &&
+	  (cd subsubmodule &&
+	   git log > ../../../expected
+	  ) &&
+	  git commit -m "added subsubmodule" &&
+	  git push
+	 ) &&
+	 (cd .git/modules/deeper/submodule/modules/subsubmodule &&
+	  git log > ../../../../../actual
+	 ) &&
+	 git add deeper/submodule &&
+	 git commit -m "update submodule" &&
+	 git push &&
+	 test_cmp actual expected
+	)
+'
+
+test_expect_success 'submodule update places git-dir in superprojects git-dir recursive' '
+	mkdir super_update_r &&
+	(cd super_update_r &&
+	 git init --bare
+	) &&
+	mkdir subsuper_update_r &&
+	(cd subsuper_update_r &&
+	 git init --bare
+	) &&
+	mkdir subsubsuper_update_r &&
+	(cd subsubsuper_update_r &&
+	 git init --bare
+	) &&
+	git clone subsubsuper_update_r subsubsuper_update_r2 &&
+	(cd subsubsuper_update_r2 &&
+	 test_commit "update_subsubsuper" file &&
+	 git push origin master
+	) &&
+	git clone subsuper_update_r subsuper_update_r2 &&
+	(cd subsuper_update_r2 &&
+	 test_commit "update_subsuper" file &&
+	 git submodule add ../subsubsuper_update_r subsubmodule &&
+	 git commit -am "subsubmodule" &&
+	 git push origin master
+	) &&
+	git clone super_update_r super_update_r2 &&
+	(cd super_update_r2 &&
+	 test_commit "update_super" file &&
+	 git submodule add ../subsuper_update_r submodule &&
+	 git commit -am "submodule" &&
+	 git push origin master
+	) &&
+	rm -rf super_update_r2 &&
+	git clone super_update_r super_update_r2 &&
+	(cd super_update_r2 &&
+	 git submodule update --init --recursive &&
+	 (cd submodule/subsubmodule &&
+	  git log > ../../expected
+	 ) &&
+	 (cd .git/modules/submodule/modules/subsubmodule
+	  git log > ../../../../../actual
+	 )
+	 test_cmp actual expected
+	)
+'
+
 test_done
diff --git a/t/t7407-submodule-foreach.sh b/t/t7407-submodule-foreach.sh
index be745fb23f..9b69fe2e14 100755
--- a/t/t7407-submodule-foreach.sh
+++ b/t/t7407-submodule-foreach.sh
@@ -118,19 +118,19 @@ test_expect_success 'use "submodule foreach" to checkout 2nd level submodule' '
 	git clone super clone2 &&
 	(
 		cd clone2 &&
-		test ! -d sub1/.git &&
-		test ! -d sub2/.git &&
-		test ! -d sub3/.git &&
-		test ! -d nested1/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub1/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub2/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub3/.git &&
+		test_must_fail git rev-parse --resolve-git-dir nested1/.git &&
 		git submodule update --init &&
-		test -d sub1/.git &&
-		test -d sub2/.git &&
-		test -d sub3/.git &&
-		test -d nested1/.git &&
-		test ! -d nested1/nested2/.git &&
+		git rev-parse --resolve-git-dir sub1/.git &&
+		git rev-parse --resolve-git-dir sub2/.git &&
+		git rev-parse --resolve-git-dir sub3/.git &&
+		git rev-parse --resolve-git-dir nested1/.git &&
+		test_must_fail git rev-parse --resolve-git-dir nested1/nested2/.git &&
 		git submodule foreach "git submodule update --init" &&
-		test -d nested1/nested2/.git &&
-		test ! -d nested1/nested2/nested3/.git
+		git rev-parse --resolve-git-dir nested1/nested1/nested2/.git
+		test_must_fail git rev-parse --resolve-git-dir nested1/nested2/nested3/.git
 	)
 '
 
@@ -138,8 +138,8 @@ test_expect_success 'use "foreach --recursive" to checkout all submodules' '
 	(
 		cd clone2 &&
 		git submodule foreach --recursive "git submodule update --init" &&
-		test -d nested1/nested2/nested3/.git &&
-		test -d nested1/nested2/nested3/submodule/.git
+		git rev-parse --resolve-git-dir nested1/nested2/nested3/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/nested3/submodule/.git
 	)
 '
 
@@ -183,18 +183,18 @@ test_expect_success 'use "update --recursive" to checkout all submodules' '
 	git clone super clone3 &&
 	(
 		cd clone3 &&
-		test ! -d sub1/.git &&
-		test ! -d sub2/.git &&
-		test ! -d sub3/.git &&
-		test ! -d nested1/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub1/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub2/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub3/.git &&
+		test_must_fail git rev-parse --resolve-git-dir nested1/.git &&
 		git submodule update --init --recursive &&
-		test -d sub1/.git &&
-		test -d sub2/.git &&
-		test -d sub3/.git &&
-		test -d nested1/.git &&
-		test -d nested1/nested2/.git &&
-		test -d nested1/nested2/nested3/.git &&
-		test -d nested1/nested2/nested3/submodule/.git
+		git rev-parse --resolve-git-dir sub1/.git &&
+		git rev-parse --resolve-git-dir sub2/.git &&
+		git rev-parse --resolve-git-dir sub3/.git &&
+		git rev-parse --resolve-git-dir nested1/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/nested3/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/nested3/submodule/.git
 	)
 '
 
@@ -247,14 +247,17 @@ test_expect_success 'ensure "status --cached --recursive" preserves the --cached
 
 test_expect_success 'use "git clone --recursive" to checkout all submodules' '
 	git clone --recursive super clone4 &&
-	test -d clone4/.git &&
-	test -d clone4/sub1/.git &&
-	test -d clone4/sub2/.git &&
-	test -d clone4/sub3/.git &&
-	test -d clone4/nested1/.git &&
-	test -d clone4/nested1/nested2/.git &&
-	test -d clone4/nested1/nested2/nested3/.git &&
-	test -d clone4/nested1/nested2/nested3/submodule/.git
+	(
+		cd clone4 &&
+		git rev-parse --resolve-git-dir .git &&
+		git rev-parse --resolve-git-dir sub1/.git &&
+		git rev-parse --resolve-git-dir sub2/.git &&
+		git rev-parse --resolve-git-dir sub3/.git &&
+		git rev-parse --resolve-git-dir nested1/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/nested3/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/nested3/submodule/.git
+	)
 '
 
 test_expect_success 'test "update --recursive" with a flag with spaces' '
@@ -262,14 +265,14 @@ test_expect_success 'test "update --recursive" with a flag with spaces' '
 	git clone super clone5 &&
 	(
 		cd clone5 &&
-		test ! -d nested1/.git &&
+		test_must_fail git rev-parse --resolve-git-dir d nested1/.git &&
 		git submodule update --init --recursive --reference="$(dirname "$PWD")/common objects" &&
-		test -d nested1/.git &&
-		test -d nested1/nested2/.git &&
-		test -d nested1/nested2/nested3/.git &&
-		test -f nested1/.git/objects/info/alternates &&
-		test -f nested1/nested2/.git/objects/info/alternates &&
-		test -f nested1/nested2/nested3/.git/objects/info/alternates
+		git rev-parse --resolve-git-dir nested1/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/nested3/.git &&
+		test -f .git/modules/nested1/objects/info/alternates &&
+		test -f .git/modules/nested1/modules/nested2/objects/info/alternates &&
+		test -f .git/modules/nested1/modules/nested2/modules/nested3/objects/info/alternates
 	)
 '
 
@@ -277,18 +280,18 @@ test_expect_success 'use "update --recursive nested1" to checkout all submodules
 	git clone super clone6 &&
 	(
 		cd clone6 &&
-		test ! -d sub1/.git &&
-		test ! -d sub2/.git &&
-		test ! -d sub3/.git &&
-		test ! -d nested1/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub1/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub2/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub3/.git &&
+		test_must_fail git rev-parse --resolve-git-dir nested1/.git &&
 		git submodule update --init --recursive -- nested1 &&
-		test ! -d sub1/.git &&
-		test ! -d sub2/.git &&
-		test ! -d sub3/.git &&
-		test -d nested1/.git &&
-		test -d nested1/nested2/.git &&
-		test -d nested1/nested2/nested3/.git &&
-		test -d nested1/nested2/nested3/submodule/.git
+		test_must_fail git rev-parse --resolve-git-dir sub1/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub2/.git &&
+		test_must_fail git rev-parse --resolve-git-dir sub3/.git &&
+		git rev-parse --resolve-git-dir nested1/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/nested3/.git &&
+		git rev-parse --resolve-git-dir nested1/nested2/nested3/submodule/.git
 	)
 '
 
diff --git a/t/t7408-submodule-reference.sh b/t/t7408-submodule-reference.sh
index cc16d3f05d..ab37c368d0 100755
--- a/t/t7408-submodule-reference.sh
+++ b/t/t7408-submodule-reference.sh
@@ -43,7 +43,7 @@ git commit -m B-super-added'
 cd "$base_dir"
 
 test_expect_success 'after add: existence of info/alternates' \
-'test `wc -l <super/sub/.git/objects/info/alternates` = 1'
+'test `wc -l <super/.git/modules/sub/objects/info/alternates` = 1'
 
 cd "$base_dir"
 
@@ -66,7 +66,7 @@ test_expect_success 'update with reference' \
 cd "$base_dir"
 
 test_expect_success 'after update: existence of info/alternates' \
-'test `wc -l <super-clone/sub/.git/objects/info/alternates` = 1'
+'test `wc -l <super-clone/.git/modules/sub/objects/info/alternates` = 1'
 
 cd "$base_dir"