I'd be frustrated too. I've never seen a wait that long. I made a bad design choice in the locking of fossil blocks and I apologize. My suggestion would be to run sync and then halt at the console, reboot, and let it start again.
There is a window (I think ten seconds) between snap -a and fossil deciding to start archiving. If you access any file in those ten seconds then enough of the root gets copied-on-write that you shouldn't see the deadlock at all. Rebooting should cause enough file activity at startup to get around the deadlock. Russ
