Oh right! In that case, GitLab's editor for comments would be what I have in mind. It doesn't have a full LaTeX implementation, so it won't allow you to download packages or use many built-in enviroments. But when writing between $` `$ it will render the text in math symbols. In that sense, the rest of the interface could remain just the same: in fact, it's not that different from this box in SourceForge.
I was actually thinking of web apps, mainly in GitLab's text editor for submitting comments in issues. It uses a Markdown version with an integrated engine wich renders math symbols. Further details are specified in the documentation. However, the engine used in GitLab works with Javascript. In the comments of this post there are links to Java libraries for TeX rendering which I believe will be better suited for Hypernomicon integration. I couldn't find any actual Java app which has this kind of...