commit-graph: stop passing in redundant repository

Many of the commit-graph related functions take in both a repository and
the object database source (directly or via `struct commit_graph`) for
which we are supposed to load such a commit-graph. In the best case this
information is simply redundant as the source already contains a
reference to its owning object database, which in turn has a reference
to its repository. In the worst case this information could even
mismatch when passing in a source that doesn't belong to the same
repository.

Refactor the code so that we only pass in the object database source in
those cases.

There is one exception though, namely `load_commit_graph_chain_fd_st()`,
which is responsible for loading a commit-graph chain. It is expected
that parts of the commit-graph chain aren't located in the same object
source as the chain file itself, but in a different one. Consequently,
this function doesn't work on the source level but on the database level
instead.

Signed-off-by: Patrick Steinhardt <ps@pks.im>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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