cocci: convert parse_tree functions to repo_ variants

cocci: convert parse_tree functions to repo_ variants

Add and apply a semantic patch to convert calls to parse_tree() and
friends to the corresponding variant that takes a repository argument,
to allow the functions that implicitly use the_repository to be retired
once all potential in-flight topics are settled and converted as well.

The changes in .c files were generated by Coccinelle, but I fixed a
whitespace bug it would have introduced to builtin/commit.c.

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