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A while ago I wrote a mini API server in order to let me leave "private comments" on a codebase.
I fully documented what it'd take to write a plugin for your favorite editor and wrote an example plugin for vim ... and then I switched to emacs.
There is a bunch of packages for this. I also have one https://github.com/thanhvg/emacs-virtual-comment
If you don't like mine then try https://github.com/blue0513/phantom-inline-comment
you might want to try out org remark