CSS caching is a perennial problem. This should be easy enough to fix with a ?TIMESTAMP, where timestamp is a number of seconds since start of last epoch when the last CSS or JS file used to generate auto-VERSION.css or auto-VERSION.js was modified. Code to generate this timestamp should be fairly easy. A couple of functions in Repository.pm for returning these timestamps and a Utils.pm function that returns the timestamp for the last modified file in a particular directory.

There is not real need to check if files are overrided in a subsequent directory or if the file modified is not CSS or JS, we just want a timestamp that does not change too often, that is removes the benefit of generally caching auto CSS and JS.