t5000, t5003: simplify commit

t5000, t5003: simplify commit

Add the whole directory of test files at once using git add instead of
calling git update-index on each of them and use git commit instead of
the plumbing commands write-tree, update-ref and commit-tree to build
the commit.  This simplifies the code considerably.

Signed-off-by: Rene Scharfe <l.s.r@web.de>
Signed-off-by: Junio C Hamano <gitster@pobox.com>