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So Logseq [1] is open (AGPLv3), also markdown with no lock in, more powerful in some key ways than Obsidian (it has block links, which I’ll let others expound on the benefit of or edit this when I’m at my desk).
The main thing it’s lacking for now is good mobile support, for which folks still use Obsidian mobile…
[1]: https://logseq.com/
FWIW - I'm a huge FOSS guy, but I went ahead and paid for Obsidian because it looked so good and it at least feels as if "saving in pure Markdown" is darn near equivalent, or at least a reasonable non-free alternative experiment; i.e. I'm not sure if this is as good as FOSS, but it's interesting enough for me to throw a few dollars at to see what happens.
In theory, seems like a fine idea. But for, me, in practice, I went back to https://zim-wiki.org (like I pretty much always do.) Not exactly sure what that says about it all, or if it much matters.
One thought though is that Obsidian feels "overloaded," almost as if it wasn't allowed to grow naturally like Zim did?
I mentioned this in another comment, but you should check out tiddlywiki[0] with the mind map plugin[1]
[0] https://tiddlywiki.com/
Same for me. I wrote a little Python script to copy my Obsidian files into a set of Hugo files, then publish them. Proprietary or not, it's so easy to work with the files that things like this are possible. It's my data in my favorite format, ready for use with all the existing text manipulation goodies I already know. There's not much to improve on there.
Plug: I wrote a couple of other scripts and put them on GitHub[1]. If you use Drafts and its "Quick Journaling" action group[2], then `process-notes` will look awfully familiar.
[1] https://github.com/kstrauser/glassknife
http://orgzly.com
Karl Voit also has a great effort going to advocate org outside of Emacs and documents some of the tools at https://gitlab.com/publicvoit/orgdown/-/blob/master/doc/Tool...
Worth mentioning here that LogSeq can work with markdown or org-mode files. In my personal setup one of my LogSeq nodes points to my BrainTool.org file which holds all my bookmarks, web-resource pointers and associated notes. This way I can bounce between working in Chrome, emacs and LogSeq all referencing the same underlying data model. (With Orgzly for a read-only view on my phone.)
See also org-roam (https://www.orgroam.com/) - an emacs-native bidirectional linking PKM solution.
It might not be a direct alternative, since it's not using markdown files directly, but I really like Trilium notes (https://github.com/zadam/trilium).
This one usually gets thrown around as a good example: https://notes.andymatuschak.org/About_these_notes
Here if you want more: https://github.com/KasperZutterman/Second-Brain
It's an interesting idea. Maybe I should try. I suspect, though, that I want control over every node, no matter how general. The thing about my notes is they contain only information I think I might need. I have, for instance, an "emotions" node. I'm sure the Wikidata node for emotions is interesting, but I want my own node too.
I tried to square this circle once by writing Hode[1], which permits encoding certain data as relevant to me, and then filter my view accordingly when I wanted. But the encoding process (i.e. the user experience when adding data to one's knowledge base) was so hard that I gave up.
[1] https://github.com/JeffreyBenjaminBrown/hode