packfile: add repository to struct `packed_git`

packfile: add repository to struct `packed_git`

The struct `packed_git` holds information regarding a packed object
file. Let's add the repository variable to this object, to represent the
repository that this packfile belongs to. This helps remove dependency
on the global `the_repository` object in `packfile.c` by simply using
repository information now readily available in the struct.

We do need to consider that a packfile could be part of the alternates
of a repository, but considering that we only have one repository struct
and also that we currently anyways use 'the_repository', we should be
OK with this change.

We also modify `alloc_packed_git` to ensure that the repository is added
to newly created `packed_git` structs. This requires modifying the
function and all its callee to pass the repository object down the
levels.

Helped-by: Taylor Blau <me@ttaylorr.com>
Signed-off-by: Karthik Nayak <karthik.188@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>