Lately I've just been using a directory full of markdown files. I store my personal collection in Dropbox but it would be just as easy to use git or any other tool. I've created an alias to automatically open that directory in my favorite editing tool when I type "notes".
I also manually maintain an index.md file to categorize things, but it's not really necessary when you can just use grep or your editors search feature to find what you need.
I do the exact same, down to the "notes" alias. I find the downside to this approach is it doesn't work well on mobile - the Dropbox app can edit files but there's no search and it all feels a bit clunky.
I also manually maintain an index.md file to categorize things, but it's not really necessary when you can just use grep or your editors search feature to find what you need.