Ask HN: How do you take notes alongside code?

I&#x27;m reading code from one of the big open source framework and finding it hard to organize notes alongside the code. I haven&#x27;t found a good way to take notes alongside the code I&#x27;m reading so I can later come back and review it.<p>My preferred way of doing it in the past has been printing out the code and writing notes alongside it in the margins but I&#x27;ve stopped doing that as it keeps wasting a lot of printer paper and ink.<p>I&#x27;m curious if anybody else has taken notes alongside code and how they are doing it, because I feel like there isn&#x27;t a good way of doing it that I know of yet.<p>I&#x27;ve also tried using org-mode in Emacs and markdown but found that a lot of editors grey out the code making it harder to see, and the whole point is to see the code since I&#x27;m reading the code and it doesn&#x27;t seem worth the effort to copy the file over to Emacs if it looks hideous. Also, I tried downloading the repository (written in C#) and opening it in Visual Studio in hopes to take notes in the form of code comments and I realized that it requires a lot of work and installations to even get the repo to compile and since I&#x27;m only wanting to read the code and take notes I don&#x27;t want to go to that effort and without getting it to compile VS makes most of the code go red with bothersome error squiggles everywhere.<p>How do you take notes alongside code? Is there a good way out there that tailors to reading code and taking notes?