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Mu has a concept of refiling which does this. I've got a load of refiling regexes set up so that I can just hold down a keypress over my inbox and it'll dynamically archive, delete messages according to my spec https://www.djcbsoftware.nl/code/mu/mu4e/Refiling-messages.h...

https://en.wikipedia.org/wiki/Procmail

procmail is the classic tool for this and can usually be wedged in somewhere.

I like maildrop (from courier) way more than procmail. I used procmail for years, but when I switched, I never looked back

Notmuch lends itself well to this. It can auto-tag new email with something like "new" and then you can write simple shell scripts to re-tag and take action based on contents.