GitLab pages, mkdocs and letsencrypt

The instructions here states that to use a LetsEncrypt SSL cert (obtained manually) with GitLab pages, the site needs to be able to serve a file like this:

http://YOURDOMAIN.org/.well-known/acme-challenge/5TBu788fW0tQ5EOwZMdu1Gv3e9C33gxjV58hVtWTbDM

but by default, mkdocs will not copy over files in hidden directories, and will attempt to style all files.

I am aware of this bug report but does anyone know of a way around this?

Thanks,

Sarah