Refactor notifications to prevent stacking.

Closes #3511, Closes #3512, Closes #3526
- show* methods now close existing passive notifications by
  default.  They also now take an optional options object where
  existing parameters such as "delayed" and "defaultErrorText"
  can be passed in as well as the new "doNotClosePassive" flag.
- Removed all explicit calls to notifications.closePassive except
  for the few places where it makes sense to call it separately.
Merge pull request #3521 from jaswilli/notifications

Prevent stacking of notifications