I changed the name of file /libraries/gantry/css/joomla.css and also made equal changings in /libraries/gantry/core/gantry.class.php and other files.
But I do not know what I have to do after renaming the files /libraries/gantry/css/joomla-ie6.css and /libraries/gantry/css/joomla-ie7.css. Are there any scripts in which I have to change code?
also I cant really see how this should be a problem since the gantry basic template is using less files that are processed into a master-xxx.css file. You can enabled compression for those files to strip css-comments ...