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RStudio’s Markdown notebooks do not suffer from this and save a separate output file that can be gitignored.

And they pay for this on other accounts:

No inline rendering of markdown.

Opening an .Rmd file is a lottery to see if rendered graphs and tables still exists.

Tables render completely differently in editor, HTML and pdf

For me, markdown is meant to be readable even when not rendered. I could see how not having persistent graphs and tables might be an issue, but my own philosophy is to start fresh each time - I treat it like a templating language with some convenient rendering features for prototyping, rather than like an IDE.

Your last point also has an upside - it's using different engines (Rmarkdown vs. Sweave). I can write whatever HTML or LaTeX code I want, depending on what's appropriate. I wouldn't want to have to make web documents with LaTeX, nor would I want to make PDFs with HTML.

> No inline rendering of markdown.

That's incorrect, take a look here -> https://blog.rstudio.com/2016/10/05/r-notebooks

RMarkdown and Knitr are dramatic improvements in terms of final outputs and VC relative to notebooks. Notebook believers (Satan worshippers, imho) would suggest that notebooks are best for developing in and not primarily made for use as final outputs.

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