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>