Categories box

A lot of options can be edited in the Admin area (in Admin - Configuration - Layout Settings)

For example, if you want to change the prefix for subdirectories (it comes as '|_' normally), you will not find it by searching the CSS files or using the Developers Tool Kit. It can be found in the Layout Settings though. It is important to be familiar with what settings are changed in the CSS and overrides, and what settings are changed in the Admin area.