linux

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rsync is like a beefed-up SCP. You'll need to write a script or cron job using rsync if you want the sync to be automatic.
Unison is great if you have the same OS and version on the machines you're syncing. It's critical that the same version of Unison is used on each machine. It's like an even more hardened version of SCP, so you'll need one of your machines to run Unison as a daemon and be able to access the other via SSH. It works best if you have a third central server, like a backup server, that each computer stays in sync with.
If you search for "keep Linux computers in sync" you'll find plenty of other tools for this as well.

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@jdlewin.eth If you want to use scripts and such programs, another option that would be best is to use the cloud, whether it be Google Drive, Ubuntu One, Dropbox, etc. and have all the files and packages ready in the cloud and they will sync them for you.