Jenkins is not able to scan the private repos in organization folder type with github app integration. Only public repos are being discovered.
How to solve this?
Are you doing a specific lab here? If so, a lab link would be very useful. My guess is that you need to register credentials for the the Github account, so the private accounts are visible to Jenkins.
What exactly do you mean by “scan a private repository”. It’s possible to add the ssh credentials to Jenkins, but since I’m unclear what “scan” means here, I’m not sure if those credentials will be used in this case.
Having gone through that CloudBees video a bit, it sounds like you got the portion on creating and setting up the credentials incorrect, since I don’t think the way he’s set up things would limit things to public repos – that’s specifically what he doesn’t want to do. But I don’t have much guidance beyond going through the portion on creating and registering the created github app. I’d look at the Repository Filter section as well.