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Description
AFAICT that solution is to add a new entry to the package DESCRIPTION telling it "it's OK to overwrite inst/doc".
However, I am working on a use case where I clone the package from the GitHub mirror (e.g. github.com/cran/xts) and then check it. The GitHub mirror contains the unpacked tar.gz version of the packages, which always has the inst/doc folder (if there are vignettes). Since I'm just running R CMD check on a git clone & then deleting the package, I definitely don't care if inst/doc gets deleted.
Essentially, I am not the package maintainer, so editing the package DESCRIPTION is a very obscure way to go about this.
For now, I will just unlink('inst/doc', recursive=TRUE) to my clone, but IMHO it would be a better design to expose some way to say "yes" to this prompt directly in rcmdcheck().