repository.c: replace hold_locked_index() with repo_hold_locked_index()

hold_locked_index() assumes the index path at $GIT_DIR/index. This is
not good for places that take an arbitrary index_state instead of
the_index, which is basically everywhere except builtin/.

Replace it with repo_hold_locked_index(). hold_locked_index() remains
as a wrapper around repo_hold_locked_index() to reduce changes in builtin/

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

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