I have Jenkins and GitHub configured like this:

1. A GitHub organization with lots of private repos, with very many branches.
2. A GitHub organization webhook with Pull Request, Push and Repository events. (Jenkins' log notes that it received a ping when the hook was set up.)
3. A Jenkins GitHub Organization folder configured to automatically trigger on branches named like .*dfiu-devops.*.

In this org, I have a git repo with no Jenkinsfile in its master branch, but with a Jenkinsfile in a branch named dfiu-devops_earlydays. When Jenkins first scanned the org, it picked up this repo and its branch. However, if I push a change to the Jenkinsfile, Jenkins does not trigger a new build of this job. If I manually trigger a new build, Jenkins does see the latest commit, but builds according to the original pipeline from the first Jenkinsfile commit. It does not update the pipeline with the new Jenkinsfile.

My first Jenkinsfile, for testing purposes, looked like this:

#!groovy

stage concurrency: 5, name: 'init'
node('docker') {
  step([$class: 'GitHubSetCommitStatusBuilder'])
  ws {
    pwd()
    sh 'pwd; find .'
  }
}

Later, I added the shell command env inside the `sh` command, but have never seen any change to the output of new builds.