Sascha Sadeghian
Could you be more specific about your Jenkins and GitHub repo configuration?
For example, do the private user repositories have the GitHub App installed? If not, then it is reasonable that the user's private repo's won't be found - the App doesn't have permission to see it.

Liam Newman

Yes, I have installed the GitHub App on my personal account, using the install guide:

https://github.com/jenkinsci/github-branch-source-plugin/blob/master/docs/github-app.adoc

I have given it read access to all repositories:

  User Account > Settings > Applications > Installed GitHub Apps > (App) > Configure

  ✓ Read access to code
  ✓ Read access to commit statuses, metadata, and pull requests
  ◉ All repositories

After the installation, the App is visible in the private repository.

  Repository > Settings > Integrations > Installed GitHub Apps > (App) > Configure

There were no further steps necessary for this. Authentication in Jenkins also works – it is just that the scan reports 0 processed repositories:

  [Tue Jun 09 16:01:58 UTC 2020] Starting organization scan...
  [Tue Jun 09 16:01:58 UTC 2020] Updating actions...
  Looking up details of $user...
  Organization URL: $full_name
  [Tue Jun 09 16:01:58 UTC 2020] Consulting GitHub Organization
  16:01:58 Connecting to https://api.github.com using xxxxx/******
  Looking up repositories of user $user
  16:01:59 0 repositories were processed
  [Tue Jun 09 16:01:59 UTC 2020] Finished organization scan. Scan took 1 sec
  Finished: SUCCESS

If I repeat the same for an organization, all private and public repos belonging to the org are found (and scanned).

Oh, I see! That helps clarify what is going on. Something is assuming orgs-only.

Sascha Sadeghian
What happens if you use an oauth token instead of app credentials?
(To do this you create a user name and password credential, but pass the token as the password.

Liam Newman

I tried the following combinations:

• Repo visibility: public | private
• Owner: profile | organization
• Authentication: username:password | username:token | GitHub App

The scan only fails for private repos owned by a profile, when authenticating via GitHub App.

Sascha Sadeghian
Thanks for the information. That will help find the code path that is causing this.

We have the exact same situation when using GitHub Enterprise 2.20+

The GitHub App Credentials in Jenkins are not usable for private repositories.

Stack Trace attached which is coming when selecting the GitHub App credentials in a multi branch pipeline job.
private-repo-stacktrace.txt

I can also confirm the bug. We are using GitHub Enterprise as well.

I used the secret from the GitHub App to manually make connections to GitHub API and it was able to retrieve internal repositories. When using the same secret with the plugin it can only find the public repos.

Tested on the latest version and 2.7.1

I was surprised that the private repositories were readable for another installation...
Now I was running into same problem and the root cause was, that the app was installed into two different organisations.
If you want to interact with a private repository, you need to set the "owner" in the GitHub App Credential in Jenkins to the particular organisation...

I think that issue is related to https://issues.jenkins-ci.org/browse/JENKINS-62220

We are on GitHub Branch Source 2.8.3

I also so have exact problems that Sascha Sadeghian is facing, any progress on this?

It seems like https://issues.jenkins.io/browse/JENKINS-62220 is the root cause for this issue.

Also see my comment here for more details https://issues.jenkins.io/browse/JENKINS-34612?focusedCommentId=401331&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-401331

I have filed a separate issue https://issues.jenkins.io/browse/JENKINS-64249 to fix documentation as it is confusing as it is right now.

I am closing this issue as duplicate in favor for 62220 - lets focus discussion there.