unpack-trees: add missing cache invalidation

Any changes to the output index should be (confusingly) marked in the
source index with invalidate_ce_path(). This is used to make sure we
still have valid untracked cache and cache-tree extensions in the end.

We do a pretty good job of invalidating except in two places.
verify_clean_subdirectory() is part of verify_absent() and
verify_absent_sparse(). The former is usually called by merged_entry()
or directly in threeway_merge(). The latter is obviously used by
sparse checkout.

In these three call sites, only merged_entry() follows up with
invalidate_ce_path(). The other two don't, but they should not trigger
this ce removal because this is about D/F conflicts [1]. But let's be
safe and invalidate_ce_path() here as well.

The second place is keep_entry() which is also used by threeway_merge()
to keep higher stage entries. In order to reuse cache-tree we need to
invalidate these paths as well. It's not a problem in the past because
whenever a higher stage entry is present, cache-tree will not be
created [2]. Now we salvage cache-tree even when higher stage entries
are present, we need more invalidation.

[1] c81935348b (Fix switching to a branch with D/F when current branch
    has file D. - 2007-03-15)

[2] This is probably too strict. We should be able to create and save
    cache-tree for the directories that do not have conflict entries
    in cache_tree_update(). And this becomes more important when
    cache-tree plays bigger role in terms of performance.

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

unpack-trees.c

@@ -1774,6 +1774,7 @@ static int verify_clean_subdirectory(const struct cache_entry *ce,
 			if (verify_uptodate(ce2, o))
 				return -1;
 			add_entry(o, ce2, CE_REMOVE, 0);
+			invalidate_ce_path(ce, o);
 			mark_ce_used(ce2, o);
 		}
 		cnt++;
@@ -2033,6 +2034,8 @@ static int keep_entry(const struct cache_entry *ce,
 		      struct unpack_trees_options *o)
 {
 	add_entry(o, ce, 0, 0);
+	if (ce_stage(ce))
+		invalidate_ce_path(ce, o);
 	return 1;
 }