object: allow clear_commit_marks_all to handle any repo

Allow callers to specify the repository to use.  Rename the function to
repo_clear_commit_marks to document its new scope.  No functional change
intended.

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