Assuming you have an ssh key for the retropie server:

Generate Docs

cd RetroPie-Setup
sudo ./retropie_packages.sh wikidocs

Deploy Docs to Server

sudo ./retropie_packages.sh wikidocs upload

PyMarkdown Fix

There is a bug with the python markdown parser where it fails to render single tables. A way to roll back is with pip:

sudo pip uninstall markdown
sudo pip install -I Markdown==2.6.7
sudo pip uninstall mkdocs
sudo pip install mkdocs==0.16.0
sudo ./retropie_packages.sh wikidocs sources
sudo ./retropie_packages.sh wikidocs build
sudo ./retropie_packages.sh wikidocs install
sudo ./retropie_packages.sh wikidocs upload

Then you have to modify the material theme to look for a max of 2.6.7