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.

Note that on first sight, this change looks like it might change the
precedence order. Before this change, we used to configure the shallow
file in the arguments handler first, and then it looks like we override
it via the environment variable. What's important to note though is the
last parameter to `set_alternate_shallow_file()`, which tells us whether
we want to overwrite a preexisting value, and when applying the value
from the environment we tell it not to overwrite preexisting values. So
in effect, the command line has precedence over the environment. After
this change, we now overwrite preexisting environment variables when we
see the argument, and consequently we keep the precedence order in tact.

With this change though we don't need the final parameter anymore that
tells `set_alternate_shallow_file()` whether or not to overwrite. We
only have a single callsite for this function now, and that function is
itself only ever called exactly once. Remove that parameter.

Signed-off-by: Patrick Steinhardt <redacted>
Signed-off-by: Junio C Hamano <redacted>