The Github desktop application fails to connect via WSS Agent and throws an authentication pop-up.
The Github desktop application uses a Basic authorization token which will be stripped by the proxy and will not be forwarded to the server.
The workaround is to bypass authentication for the domain github.com.
Login to the WSS portal and navigate to Identity > Authentication Policy > Add Auth Exemption - add a rule to bypass authentication for the domain github.com
If the WSS policies are managed from the Management Center, the following CPL policy can be used to force the proxy to forward the auth token upstream.