t4049: refocus tests

The primary thing Linus's patch wanted to change was to make sure
that 0-line change appears for a mode-only change.  Update the
first test to chmod a file that we can see in the output (limited
by --stat-count) to demonstrate it.  Also make sure to use test_chmod
and compare the index and the tree, so that we can run this test
even on a filesystem without permission bits.

Later two tests are about fixes to separate issues that were
introduced and/or uncovered by Linus's patch as a side effect, but
the issues are not related to mode-only changes.  Remove chmod from
the tests.

Signed-off-by: Junio C Hamano <gitster@pobox.com>

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