sequencer.c: remove implicit dependency on the_index

sequencer.c: remove implicit dependency on the_index

Since we're going to pass 'struct repository *' around most of the
time instead of 'struct index_state *' because most sequencer.c
operations need more than just the index, the_repository is replaced
as well in the functions that now take 'struct repository
*'. the_repository is still present in this file, but total clean up
will be done later. It's not the main focus of this patch.

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