git-sparse-checkout.txt: update to document init/set/reapply changes

git-sparse-checkout.txt: update to document init/set/reapply changes

As noted in the previous commit, using separate `init` and `set` steps
with sparse-checkout result in a number of issues.  The previous commits
made `set` able to handle the work of both commands, and enabled reapply
to tweak the {cone,sparse-index} settings.  Update the documentation to
reflect this, and mark `init` as deprecated.

Reviewed-by: Derrick Stolee <dstolee@microsoft.com>
Reviewed-by: Victoria Dye <vdye@github.com>
Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>