refs: Use *at for writes, honor repo fsync flag

refs: Use *at for writes, honor repo fsync flag

I was looking at https://bugzilla.gnome.org/show_bug.cgi?id=738954
which wants us to ensure we chown() the refs.  As part of that,
I did a generic conversion to use `*at()` (which naturally gives
us more low level control so we can call `fchown` etc.

This patch also sneaks in a change to respect the repo's
`disable_fsync` flag - if fsync is not set, then we never
`fdatasync()` (unlike the `g_file_replace_contents()` default.  Also
unlike it, if fsync is enabled, we *always* sync even if the file
didn't exist.