patch, 3 partsrun-command: optionally clear git environment

run-command.c, run-command.h

diff --git a/run-command.c b/run-command.c
index 7e779d3..5c47f45 100644
--- a/run-command.c
+++ b/run-command.c
@@ -2,6 +2,10 @@
 #include "run-command.h"
 #include "exec_cmd.h"
 
+static const char* git_env_list[] = { ALTERNATE_DB_ENVIRONMENT, DB_ENVIRONMENT,
+			CONFIG_ENVIRONMENT, GIT_DIR_ENVIRONMENT,
+			GRAFT_ENVIRONMENT, INDEX_ENVIRONMENT, NULL };
+
 static inline void close_pair(int fd[2])
 {
 	close(fd[0]);
@@ -153,6 +157,8 @@ static void prepare_run_command_v_opt(struct child_process *cmd,
 	cmd->no_stdin = opt & RUN_COMMAND_NO_STDIN ? 1 : 0;
 	cmd->git_cmd = opt & RUN_GIT_CMD ? 1 : 0;
 	cmd->stdout_to_stderr = opt & RUN_COMMAND_STDOUT_TO_STDERR ? 1 : 0;
+	if (opt & RUN_COMMAND_CLEAR_GIT_ENV)
+		cmd->env = git_env_list;
 }
 
 int run_command_v_opt(const char **argv, int opt)
diff --git a/run-command.h b/run-command.h
index 7958eb1..a5374cc 100644
--- a/run-command.h
+++ b/run-command.h
@@ -33,6 +33,7 @@ int run_command(struct child_process *);
 #define RUN_COMMAND_NO_STDIN 1
 #define RUN_GIT_CMD	     2	/*If this is to be git sub-command */
 #define RUN_COMMAND_STDOUT_TO_STDERR 4
+#define RUN_COMMAND_CLEAR_GIT_ENV	(1 << 3)
 int run_command_v_opt(const char **argv, int opt);
 int run_command_v_opt_cd(const char **argv, int opt, const char *dir);
 

Makefile, entry.c, submodules.c, submodules.h

diff --git a/Makefile b/Makefile
index c79a6da..6d24048 100644
--- a/Makefile
+++ b/Makefile
@@ -297,7 +297,7 @@ LIB_H = \
 	run-command.h strbuf.h tag.h tree.h git-compat-util.h revision.h \
 	tree-walk.h log-tree.h dir.h path-list.h unpack-trees.h builtin.h \
 	utf8.h reflog-walk.h patch-ids.h attr.h decorate.h progress.h \
-	mailmap.h remote.h
+	mailmap.h remote.h submodules.h
 
 DIFF_OBJS = \
 	diff.o diff-lib.o diffcore-break.o diffcore-order.o \
@@ -319,7 +319,8 @@ LIB_OBJS = \
 	write_or_die.o trace.o list-objects.o grep.o match-trees.o \
 	alloc.o merge-file.o path-list.o help.o unpack-trees.o $(DIFF_OBJS) \
 	color.o wt-status.o archive-zip.o archive-tar.o shallow.o utf8.o \
-	convert.o attr.o decorate.o progress.o mailmap.o symlinks.o remote.o
+	convert.o attr.o decorate.o progress.o mailmap.o symlinks.o remote.o \
+	submodules.o
 
 BUILTIN_OBJS = \
 	builtin-add.o \
diff --git a/entry.c b/entry.c
index ae64764..97f95c6 100644
--- a/entry.c
+++ b/entry.c
@@ -1,5 +1,7 @@
 #include "cache.h"
 #include "blob.h"
+#include "run-command.h"
+#include "submodules.h"
 
 static void create_directories(const char *path, const struct checkout *state)
 {
@@ -75,6 +77,31 @@ static void *read_blob_entry(struct cache_entry *ce, const char *path, unsigned
 	return NULL;
 }
 
+static int checkout_submodule(struct cache_entry *ce, const char *path, const struct checkout *state)
+{
+	const char *args[10];
+	int argc;
+	int err;
+
+	if (!is_checkedout_submodule(ce->name))
+		return 0;
+
+	argc = 0;
+	args[argc++] = "checkout";
+	if (state->force)
+	    args[argc++] = "-f";
+	args[argc++] = sha1_to_hex(ce->sha1);
+	args[argc] = NULL;
+
+	err = run_command_v_opt_cd(args, RUN_GIT_CMD|RUN_COMMAND_CLEAR_GIT_ENV,
+				   path);
+
+	if (err)
+		return error("failed to run git-checkout in submodule '%s'", path);
+
+	return 0;
+}
+
 static int write_entry(struct cache_entry *ce, char *path, const struct checkout *state, int to_tempfile)
 {
 	int fd;
@@ -193,9 +220,8 @@ int checkout_entry(struct cache_entry *ce, const struct checkout *state, char *t
 		 */
 		unlink(path);
 		if (S_ISDIR(st.st_mode)) {
-			/* If it is a gitlink, leave it alone! */
 			if (S_ISGITLINK(ntohl(ce->ce_mode)))
-				return 0;
+				return checkout_submodule(ce, path, state);
 			if (!state->force)
 				return error("%s is a directory", path);
 			remove_subtree(path);
diff --git a/submodules.c b/submodules.c
new file mode 100644
index 0000000..5baf90a
--- /dev/null
+++ b/submodules.c
@@ -0,0 +1,8 @@
+#include "cache.h"
+#include "refs.h"
+
+int is_checkedout_submodule(const char *path)
+{
+	unsigned char sha1[20];
+	return resolve_gitlink_ref(path, "HEAD", sha1) == 0;
+}
diff --git a/submodules.h b/submodules.h
new file mode 100644
index 0000000..099c4c3
--- /dev/null
+++ b/submodules.h
@@ -0,0 +1,6 @@
+#ifndef SUBMODULES_H
+#define SUBMODULES_H
+
+int is_checkedout_submodule(const char *path);
+
+#endif

diff --git a/t/t3041-subprojects-checkout.sh b/t/t3041-subprojects-checkout.sh
new file mode 100755
index 0000000..4b3cea9
--- /dev/null
+++ b/t/t3041-subprojects-checkout.sh
@@ -0,0 +1,39 @@
+#!/bin/sh
+
+test_description='submodule checkout'
+. ./test-lib.sh
+
+test_expect_success 'submodule creation' \
+    '(mkdir A && cd A &&
+      git init &&
+      echo 1 > a &&
+      git add a &&
+      git commit -m "create submodule" || exit $? )'
+
+test_expect_success 'Super module creation' \
+    'git add A &&
+     git commit -m "supermodule creation" &&
+     git branch one'
+
+test_expect_success 'submodule change' \
+    '(cd A &&
+      echo 2 > a &&
+      git add a &&
+      git commit -m "create submodule" || exit $? )'
+
+test_expect_success 'supermodule change' \
+    'git add A &&
+     git commit -m "supermodule creation"'
+
+test_expect_success 'supermodule switching branch' \
+    'git checkout one &&
+     echo 1 > expected &&
+     git diff expected A/a'
+
+test_expect_success 'supermodule reset' \
+    'git reset --hard master &&
+     echo 2 > expected &&
+     git diff expected A/a'
+
+
+test_done