presence of rmd prevents links to shiny sub folders from working

This may be related to #92. If I create an index.rmd file in the /home/user/ShinyApps folder, I can no longer access shiny apps with the server:3838/user/shiny_folder/ url. Instead, "Not Found" is shown. If instead I generate an index.html file from the rmd and then replace the rmd in /home/user/ShinyApps with the html, links work again.

Here is an example of the rmd file in /home/user/ShinyApps. The page renders fine, but not only does clicking the link show "Not Found", a direct link to server:3838/user/shiny_folder/ now also now shows "Not Found". After removing the rmd file, the direct link works again.

---
title: '`r paste("Shiny Home:", Sys.info()[["user"]])`'
output: html_document

---
* [Link](shiny_folder/)

Reproduce the problem with index.rmd in /home/user/ShinyApps and a shiny_folder/ link, then compare it with the generated index.html case. Trace how the server handles the ShinyApps directory and the /user/shiny_folder/ URL. Done means both direct and linked subfolder URLs work while index.rmd remains present.