Added annex.autoupgraderepository configuration

Can be set to false to prevent any automatic repository upgrades.

Also, removed direct mode specific upgrade code in Annex.Init, and made
needsUpgrade always include the name/path of the repo, so if
there's a problem it's clear what repo has the problem.

And, made needsUpgrade catch any exceptions that might occur during the
upgrade, so it can display a more useful error message than just the
exception.