Organizing and tagging plain text notes (macOS and iOS) For the last 5 years, I've been using a fork of Notation Velocity called nvALT 2. Truly a fantastic app.

Some of the benefits:


plain text/markdown. So I can sync the data folder via dropbox and have access to all my data on iOS or another computer. Plaintext also allows me to use TaksPaper for task management.
Sparse and performant interace. Even though I have more than a thousand notes, search is extremely fast. Creating new notes is easy.


What's becoming apparent though, is with that with such a relatively large amount of notes navigating and search is an issue. If I'm looking for a common word I get tons of hits. nvALT 2 supports rudimentary tagging but it's very basic (can't search or navigate by tags). 

What I'm looking for is an app that's similar to nvALT in spirit but supports:


hierarchical folders 
tags 


I've considered the following:


Evernote, the elephant in the room. However evernote uses a proprietary format and is slow. 
Quiver looks almost exactly like a dream note taker, but it uses a custom (though "open source") file format. It will make interop with other apps difficult.
Microsoft OneNote. Not plaintext.
SimpleNote a more basic version of nvALT with the same problems.
Apple Notes, not plain text although it would obviously sync nicely across mac and ios.


Are there any other plain text note takers with solid organization that I'm missing?
Try DEVONthink to Go for iOS, paired with one of the DEVONthink family of apps for macOS. It meets all of your criteria: it supports creating and organizing (with tags and hierarchical folders) notes in plain text, markdown, and other formats, as well as PDFs, images, and URL bookmarks. It also has a unique semantic artificial intelligence engine and other features.