I really like the idea behind Clef (and two factor authentication in general), but what I always run in to is the problem of third-party access. What do you guys recommend if you want something like Clef, but also still want to be able to use things like the WordPress mobile app, MarsEdit, etc.

The way it seems to be now is you can either secure your site with Clef (or Authy, etc), but you then either have to leave remote access password protected only or lose it altogether.

Have any of you attempted to work with the WordPress core guys on getting two-factor built in for remote access?