James Dyer has announced a new package called Simply Annotate. It is, as the name suggests, a package to make annotations to a file with the feature that the original file is not modified. There are, of course, as Dyer says plenty of packages that do this sort of thing but he wanted a light weight package that specifically met his needs and preferences.
Dyer has a list of those preferences, which you can read at his post or you can take a look at the user manual. Regardless, it appears to have some nice features. Dyer has an animation that shows how the system works. The package is available on Melpa or directly from its GitHub page. There’s plenty of information on Dyer’s post, which appears to be essentially the same as the GitHub README.
I’ve tried very hard in the past to warm up to applications like this. After all, they make perfect sense: you can make personal notes concerning the file content without altering the file itself. I spent a certain amount of time making such notes but then never—ever—actually read them. I reluctantly concluded that such things were not for me. But they may be just right for you so you should definitely take a look.