Comment out app.example.ini (#15807)

This PR is an alternative to #15559.

Instead of deleting the app.example.ini - just comment out most of the
thing. This makes it clear what needs to be set and what is completely
optional - and keeps the documentation.

The app.example.ini is moved around to move the most important settings
higher in the document.

Close #15559

Signed-off-by: Andrew Thornton <art27@cantab.net>