files-backend: avoid ref api targeting main ref store

A small step towards making files-backend work as a non-main ref store
using the newly added store-aware API.

For the record, `join` and `nm` on refs.o and files-backend.o tell me
that files-backend no longer uses functions that default to
get_main_ref_store().

I'm not yet comfortable at the idea of removing
files_assert_main_repository() (or converting REF_STORE_MAIN to
REF_STORE_WRITE). More staring and testing is required before that can
happen. Well, except peel_ref(). I'm pretty sure that function is safe.

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

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