I wholeheartedly agree with this post. I also keep my notes in Markdown, I also have plenty of Python scripting around them, including automatic publishing of my website.

I use FSNotes today on macOS and iOS. Both apps are open source, both use well-structured .textbundle directories that separate Markdown content from JSON metadata and binary attachments. Synchronization happens through Git. It's a very powerful combination.

Ironically, I wrote a blog post some 8 years ago about this very subject. That blog post is now offline.