For automation, I would like to initialize a Jenkins 2.0 instance with a pipeline job. I want to create a Groovy script that is copied to the /usr/share/jenkins/ref/init.g
If you only need to create one simple pipeline job, you can use the Jenkins API. But that really only works well when creating one simple job, for a complex setup you need some abstraction like Job DSL.
Start here: http://javadoc.jenkins-ci.org/jenkins/model/Jenkins.html#createProject(java.lang.Class,%20java.lang.String).
Example:
import jenkins.model.Jenkins
import org.jenkinsci.plugins.workflow.job.WorkflowJob
WorkflowJob job = Jenkins.instance.createProject(WorkflowJob, 'my-pipeline')
Then you need to populate the job, e.g. setting a flow definition.
Or you can wait for the System Config DSL Plugin to be ready. But it has not been released yet and I'm not sure if it can create jobs.