Best methods on storing .as files

[paragonc]

We're developing a website with multiple swf objects. Each of these objects will need access to multiple .as files. On smaller sites, i've always just stored .as files in the DocumentRoot of the website along with the swfs.

So we'd have foo.swf witch a Doc Class of Bar and Bar.as - both Bar.as and foo.swf would live in /

On this project, we are thinking about using a folder directory structure for the sake of of the home brew cms, and ease of finding items for the developers.

so it would be something like

/
/css
/flashFLA
/flashSWF
/flashFLV
/flashAS
/js
/xml
/php

Will this be more of a headache? How will this effect the way we set Doc Classes?