Before upgrade make sure you have a backup of your database if you are in production. Then replace the files with new one and restart app from pm2
pm2 restart server-linux
Android & iOS
Updating those will depend on changes done if any (This includes configurations you have done as instructed on their own sections). Using a VCS (Github, BitBucket & etc.) can help you track of changes and upgrade easily. It is necessary to use same package versions so if you have updated your server it is important that you update your Android & iOS client too with files in same version package.