How to move the bibliography in markdown/pandoc
You can place your bibliography wherever you like by inserting
::: {#refs}:::wherever you want the bibliography printed. From the "Placement of the bibliography" section of the pandoc markdown manual.
For example:
...main body# References::: {#refs}:::# Appendix
I just figured out that it works when you use a tex file, like --include-after-body=appendix.tex. I'm not an RMarkdown or Tex expert at all but I could imagine that it will only include the file after your main Rmd is already converted to a tex file using the default template.