In a startup with move-fast lightweight processes:

1. Docs that are naturally versioned with the code, like API doc or a design doc, might well go in the code repos. (I'm personally a big fan of API docs embedded in comment chunks right above the respective implementation chunk, but a separate Markdown or SVG file, or other format, also works.)

2. Everything else, one of the top priorities is to minimize friction to someone who has the information capturing it such that it can be found by someone else later, so put it in the very low-friction wiki (or an issue/task comment).

3. Have a lightweight way of cross-linking things between these locations, that everyone knows, so info is more likely to be found later.

This still applies even if you feed everything into AI now.