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I think this is my own misunderstanding. For Shiny applications, the application directory is the application; for R Markdown documents, the document is the 'application'.
Presumedly this is done to transparently handle app.R versus ui.R / server.R.
To reproduce, create a Shiny application and publish it to RStudio Connect. Then, try to forget its deployment.
rsconnect
will report:See also: rstudio/rstudio#3998.
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