Putting them in .config is something to work toward in the long term, but I like this as an immediate fix. A possible UX could be a single entry at the bottom of the repo root listing with "+ 6 hidden files, click here to show", that then expands out to to reveal the full listing when clicked.

Edit to add— someone suggests this on the linked issue, and it is mentioned as a concern that auto-hiding the files could lead to them being used to conceal malicious code. Not sure how significant of a concern that really is, but it's an interesting angle, anyway.