lib/pull: Tweak update_timeout logic again

lib/pull: Tweak update_timeout logic again

I was hitting `SIGSEGV` when running `cosa build` and narrowed it down
to #1954. What's happening here is that because we're using the default
context, when we unref it in the out path, it may not actually destroy
the `GSource` if it (the context) is still ref'ed elsewhere. So then,
we'd still get events from it if subsequent operations iterated the
context.

This patch is mostly a revert of #1954, except that we still keep a ref
on the `GSource`. That way it is always safe to destroy it afterwards.
(And I've also added a comment to explain this better.)