builtin/checkout-index: stop using `the_repository`

builtin/checkout-index: stop using `the_repository`

Remove the_repository global variable in favor of the repository
argument that gets passed in "builtin/checkout-index.c".

When `-h` is passed to the command outside a Git repository, the
`run_builtin()` will call the `cmd_checkout_index()` function with `repo`
set to NULL and then early in the function, `show_usage_with_options_if_asked()`
call will give the options help and exit.

Pass an instance of "struct index_state" available in the calling
context to both `checkout_all()` and `checkout_file()` to remove their
dependency on the global `the_repository` variable.

Mentored-by: Christian Couder <chriscool@tuxfamily.org>
Signed-off-by: Usman Akinyemi <usmanakinyemi202@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>