You want it to update each application automatically?
I don't see how you can do it in real-life, you want to log into their servers and then have PHP automatically replace old files?
This can lead to serious security flaws...
I believe that the best way is to do it manually for each application... after all, how many clients will run this application? 3,4,5?
If you still want it done automatically using some software, I think you should search for something else - not PHP. Maybe C?, Java? I really don't know.
Anyways, good luck and don't forget to update us during the whole process so we can learn from your mistakes/problems and from the good things too
P.S Maybe there is a real way to do it with PHP without any serious security flaws or any other permission issues which I'm not aware of, but currently I don't think this is the case. I'll change my mind once someone shows me a specific way/idea how this can be done with PHP.