Do not read or write git reference files directly (#18079)

Do not read or write git reference files directly (#18079)

Git will and can pack references into packfiles and therefore if you write/read the
files directly you will get false results. Instead you should use update-ref and
show-ref. To that end I have created three new functions in git/repo_commit.go that
will do this correctly.

Related #17191

Signed-off-by: Andrew Thornton <art27@cantab.net>