Have you looked into either Obsidian or Logseq?

Obsidian is not open source, but uses Markdown for notes just like Logseq. Very popular overall.

Did you know that you can use Joplin on a standard webdav server? Basically it just takes up the space of the data itself. I have it on a Caddy server and works like q charm synching between Windows and Android client

Use Nextcloud AIO mastercontainer, set up joplin with Nextcloud sync (which is webdav). Use the builtin backup function in Nextcloud AIO container to backup nextcloud and the files it contains that are your joplin notes (and anything else you use nextcloud for).

I even use Nextcloud for its Gpoddersync app to keep my podcast subs/progress from Antennapod.

Logseq. That is all. (Oh, and syncthing...)

Connect it to a DAV server and you dont have to learn a new software.

Yeah the lack of actual .md files is what killed Joplin for me. Obviously not FOSS but there are self hosted options for Obsidian.

I recently switched from Joplin to Obsidian for different reasons. I'd prefer something FOSS, but so far I've been happy with the transition. Since it works with plain markdown files, it would fit your use case

Why do you need to back up that server data? The great thing about joplin, is that the full content of your notes (and history) is distributed, like a git repo. As long as you have one device left with your notes, everything else can be bootstrapped from there. If your sync server burns down, start a new one and sync your notes to it again.

Seconding what others have already said. You should ABSOLUTELY NOT directly back up /var/lib/postgresql if that's what you're doing right now. Instead, use pg_dump: https://www.postgresql.org/docs/current/backup-dump.html

This should also give you smaller and probably more compressible backup sizes.

I think you need to learn more about how databases work. They don't typically reclaim deleted space automatically for performance reasons. Databases like to write to a single large file they can then index into. Re-writing those files is expensive so left to the DBA (you) to determine when it should be done.

And how are you backing up the database? Just backing up /var/lib/postgres? Or are you doing a pg_dump? If the former then it's possible your backups won't be coherent if you haven't stopped your database and it will contain that full history of deleted stuff. pg_dump would give you just the current data in a way that will apply properly to a new database should you need to restore

You can also consider your backup retention policy. How many backups do you need for how long?

I'm going to start developing my own alternative, is there any features that you really need/want?

I was planning on making this self hosted via docker with the option to save to Google drive.

https://github.com/ssebs/PadPal-Server

If you're after some help with the WebDAV part I set it up for myself recently and would be happy to help adapt my stuff to your stack (mine is Apache + compose, but would be about just as easy with anything else). Reply here or DM any time 💯

And good on you for being turned around on your original premise and being so gracious about it in the comments mate 👍

Joplin server also will use a file based storage instead of the db. And db then is only used for users

I use joplin as i share notes and collaborate with my wife. Obsidian etc dont do that. Id love to be on obsidian as i really like it but sharing notebooks is mandatory

Notesnook is great. Not yet self-hostable (server is open source), but they are working on it.

I self host Outline with storage connected to a Minio instance that I use as S3 storage for several applications.

I loved the ability of writing in markdown form, but a simple and intuitive design, with the ability to share a whole collection, a subset of pages, or a single page publicly without dealing with a bunch of overhead.

What is your 'deleted files' policy? How long do you keep them? I had a similar issue but then found out that the nextcloud cron-process wasn't running so files in the 'deleted files' folder where never really deleted.