@@ -2,6 +2,7 @@
 #include "blob.h"
 #include "dir.h"
 #include "streaming.h"
+#include "submodule.h"
 
 static void create_directories(const char *path, int path_len,
 			       const struct checkout *state)

@@ -146,6 +147,7 @@ static int write_entry(struct cache_entry *ce,
 	unsigned long size;
 	size_t wrote, newsize = 0;
 	struct stat st;
+	const struct submodule *sub;
 
 	if (ce_mode_s_ifmt == S_IFREG) {
 		struct stream_filter *filter = get_stream_filter(ce->name,

@@ -203,6 +205,10 @@ static int write_entry(struct cache_entry *ce,
 			return error("cannot create temporary submodule %s", path);
 		if (mkdir(path, 0777) < 0)
 			return error("cannot create submodule directory %s", path);
+		sub = submodule_from_ce(ce);
+		if (sub)
+			return submodule_move_head(ce->name,
+				NULL, oid_to_hex(&ce->oid), SUBMODULE_MOVE_HEAD_FORCE);
 		break;
 	default:
 		return error("unknown file mode for %s in index", path);

@@ -259,7 +265,31 @@ int checkout_entry(struct cache_entry *ce,
 	strbuf_add(&path, ce->name, ce_namelen(ce));
 
 	if (!check_path(path.buf, path.len, &st, state->base_dir_len)) {
+		const struct submodule *sub;
 		unsigned changed = ce_match_stat(ce, &st, CE_MATCH_IGNORE_VALID|CE_MATCH_IGNORE_SKIP_WORKTREE);
+		/*
+		 * Needs to be checked before !changed returns early,
+		 * as the possibly empty directory was not changed
+		 */
+		sub = submodule_from_ce(ce);
+		if (sub) {
+			int err;
+			if (!is_submodule_populated_gently(ce->name, &err)) {
+				struct stat sb;
+				if (lstat(ce->name, &sb))
+					die(_("could not stat file '%s'"), ce->name);
+				if (!(st.st_mode & S_IFDIR))
+					unlink_or_warn(ce->name);
+
+				return submodule_move_head(ce->name,
+					NULL, oid_to_hex(&ce->oid),
+					SUBMODULE_MOVE_HEAD_FORCE);
+			} else
+				return submodule_move_head(ce->name,
+					"HEAD", oid_to_hex(&ce->oid),
+					SUBMODULE_MOVE_HEAD_FORCE);
+		}
+
 		if (!changed)
 			return 0;
 		if (!state->force) {