I wanted to write a quick post about how I'm structuring my projects recently. I develop in Sass, so this is what this article will focus on, but the core can be applied to any preprocessor or even sites using basic CSS. (gasp!)
... /assets /sass /cavern /ui _vars.sass screen.sass /css screen.css /images logo.png /js scripts.js /fonts Local_Font.tiff index.html (php/etc..)
If you're using compass, you'll want to track this 'assets' folder. The config.rb file will get installed inside of it as well. What this allows you to do is also create a repo just for your sites theme assets. I often create them as submodules of my framework repo (Drupal, Larvel etc). I find this allows me to easily update my themes submodules as well as segment my front-end assets from my back-end ones.
I'll have more Sass, compass, and front-end architecture posts coming soon.