folder structure and readme in each folder with instructions

[vojtechhuser]

let create some empty folders and give guidance an what they should contain
(these would be OPTIONAL for researchers to adopt

e.g., protocol folder
We can then study all the protocols nicely. each study will have it in the same place.

We can have book chapter about all those optional conventions

Even guidance for when to use
workFolder
cohortSchema

so template would have how to execute templated text.
This would be great time saver.
I even suggested connectionDetails2 for this purpose

centralized processing .R script
CodeToRun .R script

shiny folder