unpack-trees: do not check for conflict entries too early

The idea of sparse checkout is conflict entries should always stay
in worktree, regardless $GIT_DIR/info/sparse-checkout. Therefore,
ce_stage(ce) usually means no CE_SKIP_WORKTREE. This is true when all
entries have been merged into the index, and identical staged entries
collapsed.

However, will_have_skip_worktree() since f1f523e (unpack-trees():
ignore worktree check outside checkout area) is also used earlier in
verify_* functions, where entries have not been merged to index yet
and ce_stage() is not zero. Checking ce_stage() then may provoke
unnecessary verification on entries outside checkout area and error
out.

This fixes part of test case "read-tree adds to worktree, dirty case".
The error

error: Untracked working tree file 'sub/added' would be overwritten by merge.

is now gone and (unfortunately) replaced by another error, which will
be addressed in the next patch.

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

unpack-trees.c

@@ -143,9 +143,6 @@ static int will_have_skip_worktree(const struct cache_entry *ce, struct unpack_t
 {
 	const char *basename;
 
-	if (ce_stage(ce))
-		return 0;
-
 	basename = strrchr(ce->name, '/');
 	basename = basename ? basename+1 : ce->name;
 	return excluded_from_list(ce->name, ce_namelen(ce), basename, NULL, o->el) <= 0;
@@ -155,7 +152,7 @@ static int apply_sparse_checkout(struct cache_entry *ce, struct unpack_trees_opt
 {
 	int was_skip_worktree = ce_skip_worktree(ce);
 
-	if (will_have_skip_worktree(ce, o))
+	if (!ce_stage(ce) && will_have_skip_worktree(ce, o))
 		ce->ce_flags |= CE_SKIP_WORKTREE;
 	else
 		ce->ce_flags &= ~CE_SKIP_WORKTREE;