The intermediate file render*.rds is cleaned up at

bookdown/R/render.R

Line 191 in ca0145f

on.exit(file.remove(render_args), add = TRUE)

If R is terminated by clicking the red Stop button in RStudio, for some reason this on.exit() is not called. @hadley I've verified that even with your fix in Improved intermediate cleanup #1079, the .rds will still be left inside the tempdir(). We need to figure out why the Stop button in RStudio kills R so brutally.

For the intermediate *.md files, they are left there if a certain Rmd fails to compile, but they will be cleaned up again the next time after you fix the error in the failing Rmd document and recompile it:

bookdown/R/render.R

Lines 222 to 223 in ca0145f

    
           intermediates = unlist(lapply(meta, attr, 'intermediates', exact = TRUE)) 
        
           if (clean) on.exit(unlink(intermediates, recursive = TRUE), add = TRUE)

Terminating build part way through book leaves many intermediate files lying around #986

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