How do I configure "Scan Multibranch Pipeline Triggers" in my jenkinsfile?

The settings on the multibranch configuration page only configure the multibranch scan job itself, not the individual jobs created inside the multibranch "folder".

The option under "Scan Multibranch Pipeline Triggers" that says "Periodically if not otherwise run" is only a trigger for when the multibranch job will scan for new branches. If changes are found to existing branches, or if new branches are discovered with a Jenkinsfile that match your branch specifications, a new build will be triggered, but this is not intended to be the way a job is triggered.

Actually, you can disable the automatic build when changes are found by adding a property to the SCM configuration to "Disable automatic SCM Triggering". Then then you will see the multibranch scan trigger, but the jobs themselves won't build, even if there are changes found.

To trigger jobs, ideally you should use a webhook if you can. If you use a git hook using the git plugin (not the github plugin), then you need to enable the PollSCM trigger (though you can set it to only poll rarely, or not at all).

If you just want normal triggering options, as of 2.22, you can configure the either cron or pollSCM triggers.

pipeline {
    triggers {
        cron('H/4 * * * 1-5')
        pollSCM('0 0 * * 0')
    }

Then I believe you can configure webhooks to inform your multibranch job when to do a scan. I haven't tried that. I just tell it to scan every hour or a couple times per day using the "Periodically if not otherwise run".

Note, the same thing applies for the build discarder and other things you configure in your multibranch job. In the web UI, you can only configure the multibranch job itself, not the individual jobs created from it. You have to use Pipeline to configure the jobs.

Using the JobDSL Jenkins Plugin for multibranch pipeline job, the periodic folder trigger can be configured as given below. In this example, the maximum amount of time since the last indexing that is allowed to elapse before an indexing is triggered will be seven days.

multibranchPipelineJob('my-awesome-job') {
    triggers {
        periodicFolderTrigger {
            interval("7d")
        }
    }
}

If your're using the JobDSL Jenkins plugin for creating jobs, then you can add following lines to configure "Scan Multibranch Pipeline Triggers":

configure {
    it / 'triggers' << 'com.cloudbees.hudson.plugins.folder.computed.PeriodicFolderTrigger'{
        spec '* * * * *'
        interval "60000"
    }
}