?bookdown::render_book says "Render multiple R Markdown files under the current working directory into a book".
Why did you do it that way?, would have not been more sensible to let the user pass the directory that contains the files?
This basically means that you have to put the files in the root of your project. You cannot have your book in a subdirectory within your project. Ok, I guess you can setwd("my_book_subdir"), but then @jennybryan comes and set your laptop on fire 
I thougth passing the index.Rmd in the subdirectory as the input argument in this function would work, but nope.
Just trying to understand here the rationale behind the decision, ..., and implicitly filing a feature request to allow a more flexible behaviour and not rely only on current working directory.
Thx