> Adding figure creation in the test qmd file, we can see that the the figure dir is in another folder containing format in the name

And so now I have it all covered. Probably another issue but related. 

The directory with format in the name is created by **rmarkdown** when R chunks are added. I don't think Quarto expect this so not sure we are cleaning this correctly. 

When no `output_file` is passed to `rmarkdown::render()`, one is automatically determined  considering the `pandoc.to` format. 

````r
# determine the output file for a pandoc conversion
pandoc_output_file <- function(input, pandoc_options) {
  to <- strsplit(pandoc_options$to, "[+-]")[[1]][[1]]
  ext <- pandoc_output_ext(pandoc_options$ext, to, input)
  output <- paste0(xfun::sans_ext(input), ext)
  basename(output)
}
````

With `to` being `customwriter.lua`, the output file will have a `.customwriter` suffix as we can see in above comments

Then the files where to store figures for **knitr** is computed based on `output_file`
````r
files_dir_slash <- file.path(output_dir, knitr_files_dir(basename(output_file)))
````

which will lead to the other folder `customwriter-yaml.customformat_files` when R code are into this. 

I believe this will happen with any format no known by rmarkdown function `pandoc_output_ext`
````r
pandoc_output_ext <- function(ext, to, input) {
  if (!is.null(ext)) return(ext)
  if (to %in% c("latex", "beamer")) return(".pdf")
  if (to %in% c("html", "html4", "html5", "s5", "slidy", "slideous", "dzslides", "revealjs"))
    return(".html")
  if (to == "markdown" && tolower(xfun::file_ext(input)) != "md") return(".md")
  paste0(".", to)
}
````

I'll probably look into that in another issue too, but that explains the behavior and differences seen above

_Originally posted by @cderv in https://github.com/quarto-dev/quarto-cli/issues/4260#issuecomment-1421667821_
            
cderv
2023-02-14T15:48:14Z
cderv
bug
v1.4
open
Specific handling for custom writer lua file for R Markdown processing
https://github.com/quarto-dev/quarto-cli/issues/4347