Before using borg I would recommend you to take a look at restic. In my opinion it is better in everything than borg.

As for how to backup the database, my advice is to export the database to a SQL file and backup that file. That will always be easier than having to deal with agents that connect to the database.

As for the number of repositories, if you use restic, a single repository is enough. Besides, as restic does deduplication, if you have the same files between your machines, they will only occupy the space of one. ;-)

I hope I have helped you with some of my ideas.

Best regards.

for the database, consider a script that does a "mysqldump" of the entire database that you schedule to run on the system daily/weekly. Also consider using gpg to encrypt the plain text file and delete the original in the same script. This is so you don't leave a copy of the data unencrypted anywhere outside the database. You can then initiate either a copy of the encrypted file to a local folder that you're backing up, or if you've set this up to back up directly on the remote that's fine too - bringing it local gives you a staged copy outside the archive and not on the original host in case you need an immediately available backup of your database.

With respect to the 3 separate repos, I would say keep them separate unless you have a large amount of duplicated data. Borg does not deduplicate over different repos as far as I'm aware. The downside of using a single repo is that the repo is locked during backups and if you're running different scripts from each host, the lock files borg creates can become stale if the script doesn't complete and one day (probably the day you're trying to restore) you'll find that borg hasn't been backing your stuff up because a lock file is holding the backup archive open due to a failed backup that terminated due to an untimely reboot months ago. I don't recall now why this occurs and doesn't self-correct but do remember concluding that if deduplication isn't a major factor, it's easier and safer to keep the borg repos separate by host. Deduplication is the only reason to combine them as far as I can tell.

When it comes to backup scripts, try to keep everything foolproof and use checks where you can to make sure the script is seeing the expected data, completes successfully and so on. Setting up automatic backups isn't a trivial task, although maybe tools like rclone and borgmatic simplify it - I haven't used those, just borg command line and scp/gpg in shell scripts. Have fun!

Personally I would create one borg repo for every server I backup. But I also use borgbase, which encourages that by default.

About the backup of the datase - use mysqldump and store that. You can also do it like this:

mysqldump [...] | borg create [...] -

The - tells borg to use stdin as the content you want to store.

Lastly there is a pull mode in borg, that way you could run one script on one host to backup all your servers. You would need to run mysqldump over ssh then.

Edit:

You can use one repo for all servers, make sure to use prefixes, so that you can use --glob-archives with borg prune, if not you might get old backups cleaned out that you want to keep.

borgmatic dev here. What I do is run borgmatic locally on each server that needs to get backed up. That's a whole lot easier IMO than setting up network filesystems / rclone or tunnels or screwing around with database dumps yourself, and potentially more reliable. So in your case, I'd run borgmatic on the VPS and then have it connect locally to your MariaDB database using borgmatic's native filesystem support. And then if you also backup the local files with that same VPS instance of borgmatic as well, there's nothing to "merge."

I'd generally recommend one Borg repository per source server / instance of borgmatic.

Lastly, my raspberry uses rclone to push to S3 and I don’t want the keys to be accessible on the VPS’s, that’s why I’m trying to have borgmatic only on my raspberry.

You could always have borgmatic backup to a local Borg repository on the VPS, and then run rclone on your trusted server to copy that repository to S3. Personally I'd probably just put the S3 keys on the VPS and lock it down so that I trust its security, but you do you. 😀