Move ref writing to be transaction-based

Move ref writing to be transaction-based

Rather than having separate write_ref calls, make clients start a
transaction, add some refs, and then commit it. While this doesn't
make it 100% atomic, it makes it easier for us to use an atomic
model, and it means we don't do as much I/O updating the summary
file and such.

https://bugzilla.gnome.org/show_bug.cgi?id=707644