I wrote a tool for myself that will just open up your default editor and create a new markdown file for every note you want to take, saving them in a git repo that you can sync to some remote. Has the simplicity of a directory full of markdown files, but also provided a system to tag the different notes, search for a particular note to view or modify, and view a subset of them in an HTML document. All of that can be done with different command line tools of course but it is nice to have it all bundled into a single program.