I often compose prompts from various sources (my "AGENTS.md", "CURRENT_TASK", "CURRENT_PHASE", ...). Last year I was composing in markdown and that got very tedious very quickly. I tried various text and text-like formats, and it turned out HTML is already one of the best formats for this, including for an "AGENTS.md" (which I keep in HTML despite the required ".md" extension).

Of course, if you build up your prompt entirely by hand (copy pasting snippets, etc.) you can get away with markdown or plain text. That works okay for some harnesses, but it leaves too much control (or more accurately, opportunity to misunderstand) to the harness.