This is a "feature request" as per this Stack Overflow comment.

I'd like to specify a specific subdirectory to contain my Rmd files. I can include the specific file names in _bookdown.yml but I'd prefer not having to update that file every time a new .Rmd file is added.

If I set rmd_subdir: true then all Rmd files from the current directory and all subdirectories are included. However, I'd love to be able to specify a single subdirectory (or an array of subdirectories) for example by adding something like

rmd_subdir: ["input/", "otherinput/"]

to _boodown.yml.