To find where the files/ directory is, look at the files_dir parameter in the config.inc.php configuration file:

[files]

; Complete path to directory to store uploaded files
; (This directory should not be directly web-accessible)
; Windows users should use forward slashes
files_dir = /usr/local/ojs-files

Back up this directory and all of its contents, e.g. if the backup should be placed in /root/:

$ cd /usr/local/ojs-files/
$ tar czf /root/ojs-files.tar.gz

When these steps have been completed, you will have created three backup files, which can be found in /root. All three of these are required to restore a copy of OJS from backup.