Vignette improvements

[thomaszwagerman]

Reviewer comments on vignettes:

• Impove main vignette introduction. From the reviewer: "The main vignette doesn't really start with an intro that clearly explains what the package is doing. The brief intro sentences may be slightly confusing. I would recommend adding another sentence or two explaining in big-picture terms what are the inputs you would need, and what outputs/results you should expect to get."
• Mention scripts are run in Bash shell.
• Hide JOSS vignette until it is ready.
• Grammar and punctuation check.

See ropensci/software-review#676

[thomaszwagerman]

Hiding vignettes is not really possible, like it is with draft quarto pages