read-cache: mark updated entries for split index

The large part of this patch just follows CE_ENTRY_CHANGED
marks. replace_index_entry() is updated to update
split_index->base->cache[] as well so base->cache[] does not reference
to a freed entry.

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

entry.c

@@ -214,6 +214,7 @@ finish:
 		if (!fstat_done)
 			lstat(ce->name, &st);
 		fill_stat_cache_info(ce, &st);
+		ce->ce_flags |= CE_UPDATE_IN_BASE;
 		state->istate->cache_changed |= CE_ENTRY_CHANGED;
 	}
 	return 0;