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

This reverts commit 16335fdd7a.

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.

builtin-commit.c

@@ -156,6 +156,8 @@ static int list_paths(struct path_list *list, const char *with_tree,
 
 	for (i = 0; i < active_nr; i++) {
 		struct cache_entry *ce = active_cache[i];
+		if (ce->ce_flags & htons(CE_UPDATE))
+			continue;
 		if (!pathspec_match(pattern, m, ce->name, 0))
 			continue;
 		path_list_insert(ce->name, list);