How do you keep your app together if you want to put some parts of it outside the document root?

[eluser]eoinmcg[/eluser]
what i usually do is something like:

/path/to/site/
|+application/
|~public/
| |+assets/
| |+uploads/
| |-index.php
| `-robots.txt
|+system/

where /path/to/site/public is the document root.
so application and system are both below the root and not publicly visible. i keep css, images, javascript etc in assets.

with this approach you can still just copy the /path/to/site/ folder to your thumb drive in one neat package.