files-backend: add and use files_ref_path()

Keep repo-related path handling in one place. This will make it easier
to add submodule/multiworktree support later.

This automatically adds the "if submodule then use the submodule version
of git_path" to other call sites too. But it does not mean those
operations are submodule-ready. Not yet.

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

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