More fixes to make no-global-lock work right

- Switch logic behind -r. Now it means the opposite, because otherwise
  there may be conditions where we stop updating repos due to multiple
  writers modifying manifest.
- Allow adjusting alternates from None to some other value. This is the
  only safe operation as far as alternates are concerned, since
  everything else would require a repack prior to operation. Might add
  that in later, but not right now.