Free and Open Source Software

TLDR: It's a mess.

Back in the day, I started migrating notepad stuff to Markdown on a Wiki. Then on a MediaWiki. Then DokuWiki. Then ZimWiki. Then Joplin. Then GitHub Pages and a self-hosted Jeckyll.

Each, single, one, of, them, uses a slightly different flavor of Markdown. At this point, I have stuff spread over ALL OF THEM, much of it rotting away in "backups to migrate later". 😮‍💨
I've been considering "vibe coding" some converters...

As for syncing... the Markdown part is easy: git.
Working with a Markdown editor to update GH Pages, was a good experience.
Having ZimWiki auto-sync to git, was good, but didn't find a decent compatible editor for Android.
I switched to Joplin lured by the built-in auto-sync options, but kind of regret it now, when it has a folder with thousands of files in it.

Obsidian is not OSS itself, but has an OSS plugin to sync to git.
I've read that using Logseq alongside Obsidian should be possible... and was planning to test that setup, keeping Obsidian in charge of sync. Possibly with GitHub/Jeckyll, git-lfs for images and attachments.

PS: assuming one could have working back-and-forth converters for the different Markdown flavors, and everything stored in git, then one could theoretically use git hooks to convert to/from whatever local version used by a particular editor.

I've bounced between a bunch of different ones. Each time I switched and moved the directory over the formatting and linking tended to break. In the end, I settled on just a raw hierarchical directory structure using raw markdown (using a basic text editor) for typed notes and whatever other relevant media (pictures, pdfs, whatever), and GoodNotes for handwritten notebooks with PDF backups saved to directory on my Nextcloud.

I don't know, maybe my needs are odd but I've just never found a single application that could handle all of my note-taking and documentation needs. Everything is close, but frustratingly annoying in one missing feature or another. And all of them seemed damned slow compared to just opening up a file browser or a terminaland doing what I needed.

As for file syncing, Logseq was pretty easy to handle syncing for. I just put the logseq notes directory on my Nextcloud and Bob's you're uncle. Access on my desktop, laptop and mobile devices. Don't have to use Nextcloud though, just something that would allow you to sync the directory between devices. Syncthing would probably work. Just don't bounce between devices too fast. Causes conflicts you have to correct manually.