Flyspray has a favicon.ico in its root folder and is found automatically by browsers if flyspray runs at webroot folder of domain. (fallback case)
If you run Flyspray in a subfolder of your domain (
www.example.com/flyspray ) or want a different favicon than the default, copy your individual favicon.ico (or favicon.gif or favicon.png if you ignore older webbrowsers) into themes/CleanFS folder of Flyspray.
It will then be detected and included by templates/CleanFS/templates/header.tpl