I use Sublime Text and put my notes in a file. I don't use file/line references but rather name the thing I'm noting (e.g. class/method/variable). Other times I

I use Sublime Text and put my notes in a file. I don't use file/line references but rather name the thing I'm noting (e.g. class/method/variable). Other times I'll use a commit and a literal string as a (nearly) unique reference.