tests: use "test_hook" for misc "mkdir -p" and "chmod" cases

tests: use "test_hook" for misc "mkdir -p" and "chmod" cases

Make use of "test_hook" in various cases that didn't fit neatly into
preceding commits. Here we need to indent blocks in addition to
changing the test code, or to make other small cosmetic changes.

Signed-off-by: Ævar Arnfjörð Bjarmason <avarab@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>