Ensured we have the right context when including.
Duh missing /
Renamed some of the files so they look like what they are... or something.
Made the second example server used in a docroot yaml file actually reference a proper test server.
Initial config must use new classes otherwise it will not work.
Altered namespace since File is now in utils.
Created a class specifically to define every important thing about a site, run commands on it and generally interact with it. Everything else has been altered to ensure there is no (limited) breakages.