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Drawing inspiration from this... has anyone experimented with ways to make their API docs more readable by agents?

Sure, llms.txt is a convention for this.

Why does the article say that’s useless?

It’s not useful if it’s never read by agents - that’s the premise of the statement.

But will agents know to send a "Accept: text/markdown" header?

Did you consider looking to see what they actually already do? There's a reason this works.