Both the hover-over and sidenotes on gwern.net are pure JS, and require no modifications to the original Markdown or generated HTML footnotes; they just run and modify the appearance clientside and degrade to the original footnotes if JS is disabled. (Obormot says feel free to contact him if you want/need any help integrating stuff.) For more on sidenotes, see https://www.gwern.net/Sidenotes
Both the hover-over and sidenotes on gwern.net are pure JS, and require no modifications to the original Markdown or generated HTML footnotes; they just run and modify the appearance clientside and degrade to the original footnotes if JS is disabled. (Obormot says feel free to contact him if you want/need any help integrating stuff.) For more on sidenotes, see https://www.gwern.net/Sidenotes