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

[eluser]jleequeen[/eluser]
I would like to keep my apps as secure as possible, so I have decided to put my application files outside the document root. In doing this, I will have two separate places where I keep my files. This creates a problem, because I usually have some css files open, some application files, javascript files, etc. It was nice when I had everything in one nice and neat package. It also made it easier to just copy the entire app to my thumb drive and take it home and pop it in and copy it to do work there. Any ideas on how to keep things together without sacrificing security? Should I put my images/js/css under the doc root to, just keeping my index.php file in the doc root?

[eluser]jleequeen[/eluser]
Anyone?

[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.