Change name of methods/ folder

[kelliemac]

The methods/ folder that houses lab-methods.Rmd, statistical-methods.Rmd, etc. often ends up housing child Rmd documents for other report sections that aren't "methods". I propose changing this folder to be called "Rmd/" (to include all child Rmd documents) and also adding a "R/" folder for source code in the form of .R files.

@asatofh and @mayerbry what do you think about this? I'm not tied to the "Rmd/" name so I'm open to other suggestions if you have them.

[mayerbry]

I agree about methods. I'm slightly concerned that multiple R/ folders at the top-level and sub-directories could cause issues, but I don't have a better idea. Maybe child-docs instead of Rmd to be more general (quarto, images), but Rmd is probably fine.

[kelliemac]

thanks @mayerbry! I like child-docs. an alternative for R/ could be src/.