Migration from Windows Xampp to Linux Server

Hello,
we are using Projqtor for quite a while now and have decided to move the hosting from a windows based xampp installation to a Unix based server (currently we are planning with Ubuntu 10.10 server, apache, php, mysql).

For the application and the database I see no problem at all. The only little concern I have is the documents transfer. Is there any documentation or means how to directly move documents and reference them automatically to the "new" directory structure?

Maybe my question has been asked before, unfortunately the search function did not give me any satisfying result.

Thank you for the great application and all your efforts.

Christian