Run java -jar /path/to/GCIDownloader.jar [arguments].  This program will create the directory downloads/<year>/<organization>/ in the current working directory.  Each file will be set to the upload date, and the directory's last modified date will be the latest date a file inside the directory was uploaded.  See below for the options.

usage: GCIDownloader [-h] -o <arg> -y <arg>
Tool to download GCI files
 -h,--help                 Display this message
 -o,--organization <arg>   Shortname of organization to download
 -y,--year <arg>           Year to download