After updating all of my plugins early last week, I'm now also seeing what appears to be at least a variant of this issue.
We have a GitHub Organization folder setup, which correctly scans our entire org. Only one of our repositories at the moment contains Jenkins files, and it used to correctly scan all branches within that repository and pickup them up. After updating last week, the branches are no longer scanned. When I check the organization scan log, I see this:
Checking branches... Getting remote branches... Checking branch
‘Jenkinsfile’ found Met criteria 1 branches were processed (query completed) 1 branches were processed Finished examining our_org_name/our_repo_name
...but we have probably 15 branches with a Jenkinsfile in them. It just so happens to be that the only branch it scanned is alphabetically the first in our repo. Going into the repository and looking at it's scan log, the scan does not happen at all. I don't recall in this setup if it is the organization or repository level scan that normally would have kicked off our build. I tested making a commit to the one branch that the org scan does detect, and that did not initiate a repository level scan.
Jesse Glick if you have any suggestions of things to test/try/log or what not I'm all ears. This is having a big impact on our teams workflow. I'll keep digging, but I suspect this is the same issue as described above as the repository level of the GitHub Org folder appears to be the same thing as a multibranch pipeline project.
Also worth nothing, when viewing the config at the repository level it has.a scan interval set at 1 day. Since this config is created by the GitHub Org folder, we can't configure it. But despite that, it's not actually running once a day. I'm looking at it right now and the last scan was when we manually kicked it off 2 days ago.