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>

apply.c

@@ -76,10 +76,12 @@ static int parse_ignorewhitespace_option(struct apply_state *state,
 }
 
 int init_apply_state(struct apply_state *state,
+		     struct repository *repo,
 		     const char *prefix)
 {
 	memset(state, 0, sizeof(*state));
 	state->prefix = prefix;
+	state->repo = repo;
 	state->apply = 1;
 	state->line_termination = '\n';
 	state->p_value = 1;