WORKAROUND After creating a job, make a build, then Manage Jenkins > Configure System > GitHub > Advanced > Re-register hooks for all jobs.

Steps to reproduce:

1. Generate personal access token on GitHub with repo and admin:repo_hook scopes.
2. Add "Secret text" credentials with the token from the previous step.
3. In Manage Jenkins > Configure System add GitHub server with credentials from the previous step.
4. Create Pipeline job.
4.1. Check "GitHub project" and specify a repository URL.
4.2. Check "GitHub hook trigger for GITScm polling."
4.3. Click "Save."

In System Log I see:

GitHub webhooks activated for job p1 with [] (events: [PUSH])

When I create Freestyle Project with repository URL and credentials specified on Source Code Management tab and "GitHub hook trigger for GITScm polling" checked, I see:

GitHub webhooks activated for job fsp1 with [GitHubRepositoryName[host=github.com,username=user,repository=repo]] (events: [PUSH])
 PING webhook received from repo <[https://github.com/user/repo]>!

I must admit that even for Freestyle project just checking "GitHub project" and specifying repository URL doesn't cut it. Which is strange. Isn't that enough info to create a webhook?

—

UPD I was about to report it again, but found this issue. So let me report again after all.

Environment: Jenkins 2.277, Docker version 18.06.3-ce build d7080c1, Debian GNU/Linux 8, GitHub API Plugin 1.122, GitHub plugin 1.32.0.

Steps to reproduce:

# docker-compose.yml
version: '3'
services:
    jenkins:
        image: jenkins/jenkins:2.277
        ports:
            - 8080:8080

$ docker-compose up

• Unlock Jenkins
• Install suggested plugins
• Create a user
• https://github.com/settings/tokens
  • Generate new token
  • Scopes: repo, admin:repo_hook
  • Generate token
• Manage Jenkins > Manage Credentials > (Jenkins/global) > Add credentials
  • Kind: Secret text
  • Scope: System
  • Secret: (the token)
  • OK
• Manage Jenkins > Manage Credentials > (Jenkins/global) Add credentials
  • Kind: Username with password
  • Scope: Global
  • Username: (email)
  • Password: (password)
• Manage Jenkins > Configure System > GitHub > Add GitHub Server > GitHub Server
  • Choose the token credentials
  • Test connection (succeeds)
  • Check Manage hooks
  • Save
• Create a public repository on GitHub with the following Jenkinsfile in the master branch:

  pipeline {
      agent any
      stages {
          stage('Stage 1') {
              steps {
                  sh 'echo $GIT_COMMIT'
              }
          }
      }
  }
  

• New Item
  • Enter an item name
  • Pipeline
  • OK
  • Check GitHub project
  • Enter the URL: https://github.com/USER/REPO
  • Check GitHub hook trigger for GITScm polling
  • Pipeline: Pipeline from SCM
  • SCM: Git
  • Repository URL: https://github.com/USER/REPO
  • Credentials: (credentials)
  • Branch specifier: */master (the default)
  • Save
• https://github.com/USER/REPO/settings/hooks

No new hooks.