JetBackup 4 and JetBackup 5 allow you to create Directories Backup Job that can backup system folders. If you are backing up system folders like /etc , /usr then these folders and files must be restored manually. You can find more information on creating a Directories Backup Job here: https://docs.jetbackup.com/v5.1/adminpanel/backupJobs.html#backup-type
Please Note: It is not recommended to copy these system folders that are created/backed up from one operating system to another different system.
