entry.c: update cache_changed if refresh_cache is set in checkout_entry()

Other fill_stat_cache_info() is on new entries, which should set
CE_ENTRY_ADDED in cache_changed, so we're safe.

Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

entry.c

@@ -210,9 +210,11 @@ static int write_entry(struct cache_entry *ce,
 
 finish:
 	if (state->refresh_cache) {
+		assert(state->istate);
 		if (!fstat_done)
 			lstat(ce->name, &st);
 		fill_stat_cache_info(ce, &st);
+		state->istate->cache_changed |= CE_ENTRY_CHANGED;
 	}
 	return 0;
 }