Refactor subdirs to use proper Config class(es)

In #705026: Allow creation of example.com/foo and example.com/bar type of sites (Part I), we introduced subdirectory support. However, we are just hooking into various tasks, rather than generating the required config files using a Provision_Config sub-class. This should be re-factored. While we're at it, maybe we can try to #2014525: Better document the relationships between Context, Config and Service classes.