Fix a test failure (t9500-*.sh) on cygwin

Fix a test failure (t9500-*.sh) on cygwin

On filesystems where it is appropriate to set core.filemode
to false, test 29 ("commitdiff(0): mode change") fails when
git-commit does not notice a file (execute) permission change.

A fix requires noting the new file execute permission in the
index with a "git update-index --chmod=+x", prior to the commit.
Add a function (note_chmod) which implements this idea, and
insert a call in each test that modifies the x permission.

Signed-off-by: Ramsay Jones <ramsay@ramsay1.demon.co.uk>
Signed-off-by: Junio C Hamano <gitster@pobox.com>