Behavior:

When I specify the rmd_subdir metadata in the _bookdown.yml, I would expect the all Rmd files be compiled in order. However, it compiles the files according to alphabetic order of the name of sub-directories.

minimal reproducible example:

Start a default bookdown project using Rstudio.
Assume the directory structure is like the following.

.... (some necessary files)
- index.Rmd
- part1
   -- 01-pre.Rmd (Remark: In this file, I only created a one-line content `# Part I: foo {-}`)
   -- 02-foo.Rmd
   -- 03-bar.Rmd
- appendix
   -- 01-appendix-pre.Rmd (Remark: In this file, I only created a one-line content `# Part II: foo {-}`)
   -- 02-appendix-a.Rmd
   -- 03-appendix-b.Rmd

And I specify the red_subdir like this.

rmd_subdir: ['part1/','appendix/']

According to guide in the usage of rmd_files, I expect the all Rmd files in the subdir part1 would be compiled first. But it turns out that the appendix is compiled first. So the final order is like

01-appendix-pre.Rmd
02-appendix-a.Rmd
03-appendix-b.Rmd
01-pre.Rmd
02-foo.Rmd
03-bar.Rmd

My current workaround is to name the subdirectories like 0part1 and 1appendix. Then each file is rendered in desired order.

output of xfun::session_info('bookdown'):

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6, RStudio 1.1.423

Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8

Package version:
  base64enc_0.1.3 bookdown_0.11   digest_0.6.18   evaluate_0.14   glue_1.3.0     
  graphics_3.4.1  grDevices_3.4.1 highr_0.6       htmltools_0.3.6 jsonlite_1.6   
  knitr_1.23      magrittr_1.5    markdown_0.8    methods_3.4.1   mime_0.6       
  Rcpp_1.0.0      rmarkdown_1.13  stats_3.4.1     stringi_1.2.4   stringr_1.3.1  
  tinytex_0.14    tools_3.4.1     utils_3.4.1     xfun_0.8        yaml_2.2.0  

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