The user account needs access to the root file system for...everything. One option to accomplish what you are talking about might be debootstrapping: https://wiki.ubuntu.com/DebootstrapChroot
I have not tried this with your application in mind. If you were to try, and following the guide, you would change the word "hardy" to coincide with your present release...for example "maverick" or "lucid."
Good luck. What you want to do sounds like it would be easy, but in truth, I don't believe it is.