restore: invalidate cache-tree when removing entries with --staged

When "git restore --staged <path>" removes a path that's in the index,
it marks the entry with CE_REMOVE, but we don't do anything to
invalidate the cache-tree. In the non-staged case, we end up in
checkout_worktree(), which calls remove_marked_cache_entries(). That
actually drops the entries from the index, as well as invalidating the
cache-tree and untracked-cache.

But with --staged, we never call checkout_worktree(), and the CE_REMOVE
entries remain. Interestingly, they are dropped when we write out the
index, but that means the resulting index is inconsistent: its
cache-tree will not match the actual entries, and running "git commit"
immediately after will create the wrong tree.

We can solve this by calling remove_marked_cache_entries() ourselves
before writing out the index. Note that we can't just hoist it out of
checkout_worktree(); that function needs to iterate over the CE_REMOVE
entries (to drop their matching worktree files) before removing them.

One curiosity about the test: without this patch, it actually triggers a
BUG() when running git-restore:

  BUG: cache-tree.c:810: new1 with flags 0x4420000 should not be in cache-tree

But in the original problem report, which used a similar recipe,
git-restore actually creates the bogus index (and the commit is created
with the wrong tree). I'm not sure why the test here behaves differently
than my out-of-suite reproduction, but what's here should catch either
symptom (and the fix corrects both cases).

Reported-by: Torsten Krah <krah.tm@gmail.com>
Signed-off-by: Jeff King <peff@peff.net>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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