Here is a list of files that you can directly modify the source of.
live/context All files in this folder can be modified. A file for each page of the public section. IE: chat select, chat page, department offline, etc..
live/functions context.php > Switch file function_global.php > General function file for public functions get_browser_local.php > File for finding information about the visitor
live/download.php
live/graphic.php
live/image.php
live/image_utility.php
live/transcript.php
live/transcript_options.php
upload.php
Please note that you can always modify every file in the templates/ and admin/templates directory.
