There is Ruby code which compiles the .md sources files into a structure of HTML files.
The Ruby code decides how the pages are laid out. CSS is used to vary the way the website looks at different screen widths - different font sizes and image sizes are used at different resolutions.
The Nu Html Checker is run over the generated HTML and CSS to check for correctness.
The generated HTML files are checked for possible computer specific filenames.
A check that all images in the source folders get converted to be images in the generated website.
Local links in the generated HTML and PHP files are checked that they are correct, and go to files inside the generated webpages. This is something that does get broken as the code changes, and also isn't immediately obvious just looking at the webpages.
A check that every page on the generated website can be reached from the home page.
rsync is run to sync any changes up to the webspace for the website.
If the files on the remote webserver are not world readable then they can't be accessed over the web.