They are not affected by the update anyway.

Signed-off-by: Johannes Schindelin <johannes.schinde...@gmx.de>
---
 builtin/receive-pack.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/builtin/receive-pack.c b/builtin/receive-pack.c
index be4172f..4ba51df 100644
--- a/builtin/receive-pack.c
+++ b/builtin/receive-pack.c
@@ -740,7 +740,7 @@ static int update_shallow_ref(struct command *cmd, struct 
shallow_info *si)
 static void merge_worktree(unsigned char *sha1)
 {
        const char *update_refresh[] = {
-               "update-index", "--refresh", NULL
+               "update-index", "--ignore-submodules", "--refresh", NULL
        };
        const char *read_tree[] = {
                "read-tree", "-u", "-m", sha1_to_hex(sha1), NULL
-- 
2.0.0.rc3.9669.g840d1f9
--
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