setup: unify setup of shallow file

setup: unify setup of shallow file

It is possible to configure an arbitrary "shallow" file via two
mechanisms, and the respective logic to handle these is split across two
locations:

  - Via the "GIT_SHALLOW_FILE" environment variable, which is handled in
    `setup_git_env_internal()`.

  - Via the global "--shallow-file=" command line option, which is
    handled in `handle_options()`.

We can rather easily unify this logic by not configuring the shallow
file in `handle_options()`, but instead overwriting the environment
variable. The environment variable itself is then handled inside of
`apply_repository_format()`, which is responsible for configuring a
discovered Git directory.

This new logic is similar in nature to how we handle the other global
options already, all of which end up setting an environment variable.
So for one this gives us more consistency. But more importantly, this
change means that `the_repository` will not contain any relevant state
anymore before we hit `apply_repository_format()` once we're at the end
of this patch series. Consequently, it will become possible for us to
completely discard `the_repository` and populate it anew.

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