I organize my notes the same way, though I have a structure of my documents: every midnight my server creates a new directory with today (06-05-Fri) which I work with. So when I need to create a file with Markor (which is very rare case), I create it there. The only issue I’m having with this system is that Markor does not work with symlinks, which I use frequently. Or maybe it’s not Markor but Android, not sure on this part.