Since you use MD files for "organising" you may have a look at Notable [1] which is Open Source and uses MD files under the hood. And you can tag your posts to organise your projects
Personally I use a combination of Bear App [2] for Mac to organize my Notes. Bear has a built in tag function which is really easy to use. Also I'm a huge fan of it's minimalistic design. For ToDos I use Things 3 [3] which let's you categorize your ToDos in different projects.
But both are Mac only currently which is a pain point at work where I use Windows.