If we want the top-level .Rmd file to be rendered to the doc/paper directory, then this output directory needs to be configurable as an option. However, apparently it isn't; only the directory for figure output can be set. This means that rendering the Markdown, HTML, LaTeX, and PDF versions need to be executed as rmarkdown::render() so that the output path can be passed as an argument. That the "Knit HTML" button is not to be used is likely rather undesirable for practical use and teaching purposes.
If we want the top-level
.Rmdfile to be rendered to thedoc/paperdirectory, then this output directory needs to be configurable as an option. However, apparently it isn't; only the directory for figure output can be set. This means that rendering the Markdown, HTML, LaTeX, and PDF versions need to be executed asrmarkdown::render()so that the output path can be passed as an argument. That the "Knit HTML" button is not to be used is likely rather undesirable for practical use and teaching purposes.