What note-taking app are you using currently, if any?
I've been using Silverbullet [1] for a while now and love it due to it's usage of plain-text markdown files in a normal directory structure to actually store the notes. Yet, it supports many other features such as query language and to a certain extent, federation with other SilverBullet instances. The only major downside for me is that whilst it's usable on mobile, it feels cramped.
[0]: https://silverbullet.md