safe.directory: use git_protected_config()

Use git_protected_config() to read `safe.directory` instead of
read_very_early_config(), making it 'protected configuration only'.

As a result, `safe.directory` now respects "-c", so update the tests and
docs accordingly. It used to ignore "-c" due to how it was implemented,
not because of security or correctness concerns [1].

[1] https://lore.kernel.org/git/xmqqlevabcsu.fsf@gitster.g/

Signed-off-by: Glen Choo <chooglen@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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