Add back manual interleaving, but this time in Mux.

Add back manual interleaving, but this time in Mux.

We need to interleave ourselves because we flush; otherwise, audio will
typically start 100 ms or so into the stream, and everything becomes bad.
Thankfully, we have only two streams to interleave, so we can choose
something quite simple, and this is still not bothered by the deadlocks
that arose from doing it in QuickSyncEncoder. (Hopefully we can soon find
keyframe boundaries without flushing, but it requires changes in avformat.)

Also fixes an issue where plugged packets would cause the boundaries
to fall in the wrong places.