This is a small issue, but as part of a quarto website I was building for a project I wanted to include a shiny app (app.R) and a data file (cmap.arrow). I wanted to make this work with the quarto render approach. I used rsync instead of quarto publish to push the site to a shiny server.

It turns out that quarto has thought of many things, including this use case. In the _quarto.yml file that is used for details on the website you can include a clause for additional resources to bring along:

project:
    output-dir: public
    type: website
    resources:
        - "reports/Explorer/app.R"
        - "reports/Explorer/cmap.arrow"

With that small addition, quarto render will include these in the public directory during rendering. From here, I just rsync the public directory to the shiny server and I have both the shiny app and static webpages co-existing.