These last options are only available from the expert menu (accessible by hitting x from in AppleJack's main menu), and should be considered experimental at this point.
Took a quick look today, but only stuck around long enough to copy down the "menu" items:
[0] deep clean cache files  (Allows you to run the deep clean without having to run AUTO)
[1] check hard drive integrity  (Not implemented yet. Can't get smartctl to work on all drives.)
[2] test memory
[3] bless system folder  (Not implemented yet. Can't test adequately on my machine.)
[4] disable auto login
[5] disable login items for a user
[6] restore netinfo database from backup
[7] disable system configuration files
[8] disable NetInfo NFS mounts  (Only if you've set them up in NetInfo rather than fstab)
[9] enable new machine setup
[Hmm, i guess that much was in the ReadMe as well.
Have added the author's own comments above in green.]
