Drop the intermediate files *.knit.md and *.utf8.md

[yihui]

In rmarkdown, we used to generate the intermediate file *.knit.md from knitr::knit(), and convert it to another intermediate file *.utf8.md. Then pass the utf8 file to Pandoc (because Pandoc only accepts UTF-8 input).

Since knitr 1.24, knitr::knit() only accepts UTF-8 input. Since rmarkdown 2.0, functions in rmarkdown also only accept UTF-8. It makes little sense to generate these two intermediate files now (e.g. d8fbf4c makes an unnecessary file copy), and I suggest that we stop generating them in a future version.

Additional benefits:

1. blogdown users no longer needs to ignore these files: https://github.com/rstudio/blogdown/blob/a6c92734/R/check.R#L51 It may also avoid the unnecessary refreshing of Hugo server.
2. bookdown users won't see these intermediate files, either: Terminating build part way through book leaves many intermediate files lying around bookdown#986

[cderv]

*.knit.md is used for giving a name to the output file after knitting the input.
I would think that we need to keep this intermediates that knitr will write and will be the entry file for Pandoc, and that we need to remove after a render().

For now, I opened a draft PR for some more test by only removing the *.utf8.md

[yihui]

For *.knit.md, I was thinking that we could just use the single extension *.md. This would solve the bookdown issue. However, it will be problematic for blogdown (it's easy to specify that Hugo should ignore *.knit.md, but not easy to ignore *.md since not all *.md files should be ignored).

I guess we can either keep *.knit.md, or add an option to specify the extension (e.g., options(rmarkdown.knit.ext = '.md') can be used for bookdown, and options(rmarkdown.knit.ext = '.md~') for blogdown since Hugo automatically ignores files that end with ~). What do you think?

[cderv]

I am not quite sure why it will fix the issue for bookdown. Knitting the Rmd will still produce a .md file used for the HTML conversion. This file is not to keep and should be removed (unless keep_md is true).
I find it quit informative to have this file labelle *.knit.md, you know it comes from the knitting process in render. Otherwise, test.Rmd will lead to test.md then test.html.
it is highly possible that a test.md file exist in the working directory already and I am not sure we want to overwrite this one. This is because we render everything in the working dir by default so we need to be careful with filename.

I may have missed why this is an issue for bookdown because the file would still be there but with a different name. Can you (re)explain please?

The options mechanism you suggest would allow to modify behavior for different package.

[yihui]

You are right about bookdown. The intermediate *.md file will still be there. The problem won't be completely solved (with the PR #2098, it only reduces one intermediate file).

Let's keep *.knit.md. If it's easy enough, let's also add a global option for blogdown to customize the intermediate file extension.

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