setup: create ref and object databases after config is written

When creating a new repository we create both the reference and object
databases after we have finalized the repository. This ensures that
those subsystems find a fully-configured repository at the time where
they are asked to create their own on-disk data structures.

There is one exception though: while we have already fully configured
the repository at this point, we haven't yet written both
"core.sharedRepository" and "receive.denyNonFastforwards". The latter
configuration doesn't really matter to us, but the first one does as the
"files" object database source reads it.

This doesn't cause any problems right now, but it will in a subsequent
patch where we will start to read "core.ignoreCase" when creating the
object database. Move the initialization of both of these data
structures towards the end of `init_db()`. The only thing that now comes
after is status reporting, but that's it.

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

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