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>

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