Big no-no to Joplin for me is that it is using some custom data format (sqlite I think). Why bother? Just give me an app that can handle nicely markdown files, syncing I can do myself e.g. (Synology, rsync) or use some file syncing service (Dropbox, OneDrive, whatever).
Zettlr does the trick for me without interfering with what I write.
"Custom" would be the way Apple Notes or Evernote stores their data in opaque binary blobs. SQLite is standard and you can open it with plenty of third-party tools, but I see your point about plain text files being more convenient for certain tasks.
I sync Joplin via Dropbox across phone and 2 laptops. In theory a prob? But in practice rare to never bc im only one user on one device at a time. And im making small changes at a time. There was 1 minor conflict once and Joplin saw it and i quickly resolved it.
I wrote my own note-keeping system[0] and very much wanted all of the notes to just be markdown files on the disk. It turns out that there are trade-offs to this. If you want plaintext markdown files on disk AND want fancy features like file versioning, a search index, tags, etc then you need to store all of that metadata somewhere and you're down writing a half-assed implementation of a DBMS.
Now, you can certainly bite the bullet and full-ass the implementation like Dokuwiki did, but that is really quite a lot of work and effort against simply `import sqlite` and writing a couple of tutorial-level queries. And it turns out that exporting all of your documents to plaintext, if you should so choose, is a one-line command away.
I was never able to get encrypted syncing working with Joplin. I tried every year or something for a while but it never worked. I kept looking for an Evernote alternative for years. The closest that got there is Leanote, which is a Chinese company's open source product. (https://github.com/leanote)
I finally gave up the search. Switched to unencrypted plain text md files synced with syncthing. On Linux I use Kate. It has a directory tree view and recursive search in said directories. It works great. On Android I am using Markor to point to the same shared directory. I don't think I'll ever start looking for a note taking app again. I also found I don't really take notes much. So there's that. :)
It really is very good. What made me not stick with it? Trying to remember. I think it was the fact that it is a little heavy and support/issues is in Chinese, which I don't speak. Later I simplified my setup and made everything local markdown files, handling sync myself.
You can actually try their hosted service for free. Though looking at it now, most of that is in Chinese too.
> Just give me an app that can handle nicely markdown files
You know what does that well? The filesystem.
I've tested pretty much all note-taking software out there. What ended up working for me is a bunch of markdown files inside folders, synced using Github.
I have search, formatting and preview thanks to VSCode, and I can access my notes on any machine that syncs with Github.
> Why bother? Just give me an app that can handle nicely markdown files
Markdown (and any other markup) really sucks for anything that is more than just plaintext with some formatting. The best markdown-app we have at the moment are those like Obsidian or Logseq, and they are very low-key compared with a proper richtext-app, like Notion or even a mature word processor.
And looking and the hard struggle of obsidian and their community-plugins, it might be really time to get a proper open richtext-format for the notes-space, to liberate us from markups and their limitations. Maybe something json-based, to bring the notebook-movement into the ring too.
Zettlr does the trick for me without interfering with what I write.