$mainindex is a new variable that we created for use in config.php. A default value of index.php is assigned to this variable, and acts as the main index page. Perhaps you wish to use cms.php instead of index.php for your homepage and calls to modules. Simply change the value of $mainindex in config.php and rename the file index.php to the name of your choice.
While developing CPG-Nuke, we moved all functions from modules.php to index.php. Thus, the call for a module changed from modules.php?name= to index.php?name=.
However, we left modules.php in place for compatibility with third party addons and themes.