Jenkins v1 and the old Cloudbees plugin has support for a Custom Marker File filter on the Github Organization configuration. This was useful when common Pipeline Script was utilized by all projects in an organization. 

Currently in Jenkins v2, there is no way to avoid adding at least a default Jenkinsfile in each repository and calling back into the same shared Pipeline Script.

Adding support for a Custom Marker File again (with an associated default Jenkinsfile contents) would help avoid snowflake Groovy scripts by repository where not necessary