I don't know if this is a bug or WAD but I'm curious about it. I created an rmarkdown website with a navbar (specified in _site.yml). When the site is rendered, the navbar appears in source files which are physically present in the directory but it does not show up in source files which only exist in that directory as a symlink (created with ln -s). The symlink files otherwise are processed as expected.
So I'm curious: if foo.Rmd is a soft link, why doesn't foo.html get a navbar, even though it is created?
To duplicate, take this test website: https://github.com/rstudio/rmarkdown-website-examples/tree/master/common-elements . Move both about.Rmd and sessioninfo.Rmd into a new subdirectory, subdir. Create symlinks to both files in the main directory and render the site. Everything works except that about.html does not have a navbar.