Hacking on a bus to Canberra for LCA2013, I made the webapp's UI for pausing syncing to a repository also work for the local repository. This pauses the watcher thread. (There's also an annex.autocommit config setting for this.)

Ironically, this didn't turn out to the use the thread manager I built yesterday. I am not sure that a ThreadKilled exception would never be masked in the watcher thread. (There is some overly broad exception handling in git-annex that dates to back before I quite understood haskell exceptions.)