commit-graph: pass a 'struct repository *' in more places

commit-graph: pass a 'struct repository *' in more places

In a future commit, some commit-graph internals will want access to
'r->settings', but we only have the 'struct object_directory *'
corresponding to that repository.

Add an additional parameter to pass the repository around in more
places.

Signed-off-by: Taylor Blau <me@ttaylorr.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>