Although it is usually not done with /usr/*, it is quite common to put a server's /etc under version control. But that's for administrative control, and is usually completely separate from the web application.
However, it is quite common to use rsync for deployment of everything: system, application, etc. from test to production, without any version control needed. This works especially well when using vservers.
However, it is quite common to use rsync for deployment of everything: system, application, etc. from test to production, without any version control needed. This works especially well when using vservers.