Script Folder Structure
This explanations is for all versions from 1.0. and newer.
The idea is, that all your page files are included into the phpRecDB theme folder (to be exact: included in a particular theme).
There is only one file (index.php) left outside the phpRecDB-folder. This file simply starts phpRecDB and setting the correct theme. Now the complete site is working inside this particular phpRecDB-theme.
You can see a example file structure on this picture:

