I know this says "Solved" but you should look into Gitjournal. You can use the one free private repo from gitlab to connect to. Just use vscode or similar on PC and Gitjournal on your phone. Version controlled notes, file based instead of database, can organize on PC via folders (Gitjournal recognizes the folders, don't think it can create them though). I absolutely love it.

https://gitjournal.io/

emacs + org mode.

You can sync the notes files with any app of your choosing (OneDrive, Google Drive, Nextcloud, Syncthing).

Checkout Notesnook. I've tried most of the ones you've listed and have been really enjoying how well it works compared to the competition considering its end-to-end encrypted.

A few features:

• Clients and server are open source.
• End-to-end encrypted note syncing.
• You can publish public notes.
• You can publish privates notes that require a password to view.
• You can self-host the sync server.
• You can self-host the publishing server.
• Full offline mode.
• At rest encryption.
• Multi-platform clients with feature parity (Android, iOS, Linux, Windows, MacOS, Web).
• Most if not all of the general features you'd expect from a notes taking application.

One thing I really like about the project is how open they are about what they're doing, why they're doing it and what the future holds. It's been great seeing their roadmap (https://notesnook.com/roadmap/) and seeing promised features land with new ones being added, and I've only been using it for less than a year now!

Just use obsidian with sync thing.

Beware of Joplin: saved files ate not native MD files. They have MD extension but internally are quite different.

Still plain text files in a way, but not usable with a different editor easily.

This seems to be the most common question in this sub...

Results from me asking this 1Y ago: https://lemm.ee/post/4593760

Went with Joplin and using it since.

Results from the same question 2 months ago: https://lemm.ee/post/45943693

Results from the same question 1 months ago: https://lemmy.world/post/22885340

So you dislike external sync options but also don't want to pay for internal sync options? Additionally you are in a self hosted community so you're looking for a presumably open source project (some you listed are not), and given internally supported sync services would be one way fund development i think this narrows what your are looking for by quite a bit. You basically would be looking for an open source project that meets all your other criteria and happens to let you sync the files to your own server for free. Why would such a project not just let you take things into your own hands with whatever flavor of sync/backup you prefer? Otherwise if they're building a sync system it would probably be a monetized cloud service which brings us back to the beginning.

Maybe such a thing exists, but I haven't seen such a thing since that is extra development for little to no gain. Most people are happy to either pay for the cloud service to fund development or sync on their own.

Logseq: Same issues as with obsidian: Paid sync. Didnt look much beyond

Logseq is open source. Obsidian is not. So yes, both have paid sync but you can also just sync or backup the files on your own. Just be careful of sync services that sync while files/db are in use to avoid conflicts.

I can still recommend you Logseq and Obsidian.

They store their database mostly as plain markdown, so you can just use your sync app of choice (Nextcloud, Syncthing, etc.) to sync everything between devices.

Maybe Logseq offers their sync as self hostable service too, I don't know.

I find Logseq extremely awesome and would recommend it to you.

I just sync a folder with syncthing and use native markdown editors.

On a desktop I like zettlr. On android I like zettel notes. Both have zettelkasten features which is pretty much just a way to link to other files.

I've been using silverbullet for a while. Selfhosted, saves everything on simple markdown files and easy to customize with plugins and space scripts.

I use Obsidian primarily and just push everything to git. Remember to gitignore .obsidian/workspaces.json to prevent conflicts on multiple devices.

I just use Joplin, encrypted, and synced through dropbox. Tried logseq, but never really figured out how to use its features effectively. The notebook/note model of Joplin seems more natural to me. My coding/scripting stuff mostly just goes into git repos.

Another vote for Silverbullet, I've been using it for a while and it's great. There is a tree view plugin that's very easy to install, however I disabled it after a short while because I realized that, because of the way I take notes, that is a lot less useful than other features.

For example, I have a folder with all my cooking recipes, at first I thought having a Tree view would be good there, but actually if I use the querying mechanism I can have tables that give me more information than just the name, e.g. tags, difficulty, etc. also this works regardless of where the recipes are, so if I want to create a subfolder structure or scrap recipes from elsewhere in the whole space it would work (granted, not very useful for recipes, but I also have a table for work tools, some of which are embebed on another page, some of which are a page of their own, and I have a table that lists all of the tools to give me an overview)

You are posting in self hosted by also referencing some software that isn't so I'm not sure exactly what you're asking for in that regard.

Saber is the only non-onenote notes software that supports handwriting and is fully FOSS, to my knowledge. I use that and then back up with Syncthing.

I actually only discovered silverbullet a few days ago, but liking it so far.

The TreeView plugin is documented here: https://silverbullet.md/Plugs/TreeView

Regarding Joplin: I don't know what you mean by callouts, but it does have a plug-in system. Perhaps there is one containing what you need?

If not, and it's not beyond your skill set, you could build it yourself.

I didn't read the entire wall of text but didn't see it listed. check out notesnook.

I just use Obsidian + Syncthing + MEGA. My obsidian folders are on my mega synced folder on my pc, and they are set up to use syncthing to push updates to all my other devices (2 phones and a tablet), but you can have as many devices as you want. It's all free as well, and the cloud service can be any that you like.