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We are about to begin work on an application that will eventually be deployed many times on one server. I am hoping to build a nice interface so that one of my coworkers can easily create new deployments of this application. The idea is to create a wizard with a series of options that will configure basic properties of each particular copy of the app such as color scheme, domain name, etc. Each copy of the application may be further tweaked independently down the line. I would like to know what is the best way to manage the automatic creation of users, the updating of domain name info and the deploying of copies of an application, with the ability to maintain certain discrepancies between each of these copies (such as installed plugins, different CSS) as we update the application in the future.

What I'm asking is extremely similar to the way StackExchange 1.0 functioned, where a user could configure several options and a customized version of the StackExchange would soon be up and running. How is this accomplished?

A: 

One thing you can do is have the web server set a variable based on the domain name and path, and then you can check $_SERVER for the value and choose the configuration based on that. Or if the application will only be run once per domain then just check $_SERVER['HTTP_HOST'].

Ignacio Vazquez-Abrams
That sounds like a good start.
Oren