Revert "builtin-commit.c: remove useless check added by faulty cut and paste"

This reverts commit 16335fdd7ace78a8285ba25fd7a81177a48e7c9b. We are calling overlay_tree_on_cache() which does use CE_UPDATE flag to mark duplicated entries, which is the same as the codepath in git-ls-files with its --with-tree option. Because the pathname ce->name is given to path_list_insert() which does not allow duplicates, there is no breakage either way from the correctness point of view in this codepath, unlike the one in ls-files. But avoiding unnecessary processing with a single bit check is certainly better.