After upgrading all the plugins on our Jenkins server (many months of updates), the periodic scan of our Github organisation is now behaving oddly: it doesn't pick up all our branches, and within each repository it seems to stop as soon as it hits a branch with a Jenkinsfile. For example:

Organization URL: SKA Africa
[Thu Aug 23 11:39:17 UTC 2018] Consulting GitHub Organization
11:39:17 Connecting to https://api.github.com with no credentials, anonymous access
<snip lots of ignoring>
Examining ska-sa/spead2

  Checking branches...

  Getting remote branches...

    Checking branch gcc_static_link_hack
      ‘Makefile.am’ not found
    Does not meet criteria

    Checking branch master
      ‘Makefile.am’ found
    Met criteria

  2 branches were processed (query completed)

  2 branches were processed

Finished examining ska-sa/spead2

There are more branches of ska-sa/spead2 but they're not checked.

I've set up a brand new Jenkins install (from Docker) on my laptop to confirm this behaviour, so it's not just some gremlin left over from the upgrade.

Steps to reproduce:

1. Start a fresh Jenkins from jenkins/jenkins:2.121.3 Docker image, run the wizard with default options.
2. Add a Github organisation project. No credentials (we use creds in production, this is just for a test), organisation ska-sa, repository filter spead2, change the recogniser to Makefile.am (obviously that's not going to be valid Groovy, but it's just to demonstrate the issue since the organisation doesn't have a suitable public repository).
3. Look for the above in the scan.

I haven't checked it on this toy Jenkins instance, but on our production Jenkins, scanning a single repository does pick up all the branches.

I tried poking through the code to try to figure out why that might be happening or which plugin is responsible, but I got lost in the web of inter-plugin calls so I've listed a few plugins that seemed like they might have some role. As far as I got was that this line seems to be where it bails out, which I think implies that SCMHeadObserver.isObserving returned false, but I'm not too sure what SCMHeadObserver subclass is in use at the time.