So, I suppose this is quite a general question, but how does one track masked afflictions with an automatic system? Is there any way other than to check DIAG, or knowing that it means you need to eat pennyroyal (example)? Thanks.

It depends on what the masked affliction is. For example, if someone throws a Moon tarot at you (which causes mental afflictions), you can simply trigger it to do focus mind and you'll probably be alright. However, if someone tosses 6 hexes at you, you should probably focus mind and then diagnose soon afterwards.

You can try to do this after every masked message-

eat/writhe/smoke/drink/stand/insomnia

It'll catch some of the deadlier afflictions, but it's not going to work otherwise on almost everything else.

With angels and demons it's easy, since each of the specific messages is only used for one or two afflictions, the rest are useless and disused. Up to you to figure out which.

Moon gives one out of four afflictions: Amnesia, stupidity, confusion or hypersomnia.

Heretic and Infidel go best by sipping choleric and eating pennyroyal.

Fool tarot works by sipping quicksilver and writhing.

If you're getting stung, it's bet to just diagnose once in a while.

For slaughs you sip choleric and apply liniment, Crones you eat pennyroyal and/or horehound.

Telepathy should cause you to eat pennyroyal, kombu and focus mind.

Etc.. it's relatively easy to figure out with some practice.

I suggest eating kombu or marjoram with slaugh too in addition to applying liniment and sipping choleric. It can give epilepsy or rigormortis

Since rigormortis can be instantly cured when it hits (eat marjoram/apply mending), I tend to eat kombu because being knocked off balance seems worse to me.