How to organize Rmarkdown files (with Shiny runtime) inside a package

Currently I have an analysis project which I treated as package. So currently I have the following structure:

mycoolanalysispackage/
|-- .Rbuildignore
|-- .gitignore
|-- DESCRIPTION
|-- NAMESPACE
|-- inst
|-- vignettes
|-- R
`-- mycoolanalysispackage.Rproj

At the end I usually produce many Shiny applications as Rmarkdown-flexdashboard file with Shiny runtime.

  -- app1/
       |-- index.Rmd
  -- app2/
       |-- index.Rmd

My question is, in which package subdirectory should I put those application directories (along with their index.Rmd files)?

I also have local Shiny Server, what's the best way to link that Rmarkdown-flexdashboard app to that server?