@djagerif Great question! From my experience the best way would be to navigate to the directory where the files are stored and run the following command (if your using git):
git pullIf you are not simply re-download and extract/overwrite all the files. I do not provide a config.php in the repository nor do I provide the pass_file, log_file, or log_previous file so they will never be overwritten on an update/overwrite.