Provide Extensive documentation for Shiny App


some colleagues and I have built a fairly complex Shiny app that allows users upload their own data or pull in data from a number of public sources, run some statistical models on that data, and then visualize various results within the app as well as exporting results to be used outside the app.

So far we've been documenting how to use the application within the shiny app by including a page of markdown strings.

given that we need to document a pretty large number of features, the current documentation structure is getting a little overgrown and we'd like to switch from the simple markdown incorporated into the app to a more user friendly structure that includes a navigable table of contents along the left of the page. Rmarkdown allows this fairly easily but it's unclear how to include that in the shiny app as I've only found info on including markdown, not Rmarkdown. So far it seems that table of contents options in simple markdown are fairly limited.

Is anyone aware of a shiny app that is fully documented within the app? Is there a best practice to provide documentation to users in this situation?

We would prefer not to host the documentation separately from the app itself.

Thanks for any and all suggestions.

edit: to clarify further the problem, looking at the example apps, they are structured basically as linear documents with a shiny app embedded at some point in the progression, because of the extent of the documentation we need to include, we really would prefer to include it as it's own page, rather than context around a shiny app embedded into it.