packfile: fix approximation of object counts

When approximating the number of objects in a repository we only take
into account two data sources, the multi-pack index and the packfile
indices, as both of these data structures allow us to easily figure out
how many objects they contain.

But the way we currently approximate the number of objects is broken in
presence of a multi-pack index. This is due to two separate reasons:

  - We have recently introduced initial infrastructure for incremental
    multi-pack indices. Starting with that series, `num_objects` only
    counts the number of objects of a specific layer of the MIDX chain,
    so we do not take into account objects from parent layers.

    This issue is fixed by adding `num_objects_in_base`, which contains
    the sum of all objects in previous layers.

  - When using the multi-pack index we may count objects contained in
    packfiles twice: once via the multi-pack index, but then we again
    count them via the packfile itself.

    This issue is fixed by skipping any packfiles that have an MIDX.

Overall, given that we _always_ count the packs, we can only end up
overestimating the number of objects, and the overestimation is limited
to a factor of two at most.

The consequences of those issues are very limited though, as we only
approximate object counts in a small number of cases:

  - When writing a commit-graph we use the approximate object count to
    display the upper limit of a progress display.

  - In `repo_find_unique_abbrev_r()` we use it to specify a lower limit
    of how many hex digits we want to abbreviate to. Given that we use
    power-of-two here to derive the lower limit we may end up with an
    abbreviated hash that is one digit longer than required.

  - In `estimate_repack_memory()` we may end up overestimating how much
    memory a repack needs to pack objects. Conseuqently, we may end up
    dropping some packfiles from a repack.

None of these are really game-changing. But it's nice to fix those
issues regardless.

While at it, convert the code to use `repo_for_each_pack()`.
Furthermore, use `odb_prepare_alternates()` instead of explicitly
preparing the packfile store. We really only want to prepare the object
database sources, and `get_multi_pack_index()` already knows to prepare
the packfile store for us.

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

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