apply.c: make init_apply_state() take a struct repository

apply.c: make init_apply_state() take a struct repository

We're moving away from the_index in this code. "struct index_state *"
could be added to struct apply_state. But let's aim long term and put
struct repository here instead so that we could even avoid more global
states in the future. The index will be available via
apply_state->repo->index.

Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>