GitHub Organization Job
JTE can be used to apply a pipeline template to an entire GitHub Organization by creating a GitHub Organization job in Jenkins.
To configure this, under the Projects section you will set the Project Recognizer as Jenkins Templating Engine.
Exclude Branches Without pipeline_config.groovy
When Jenkins Templating Engine is selected, a checkbox option is presented to exclude branches in source code repositories that do not have a pipeline_config.groovy file at the root of the repository.
The default value is to create pipeline jobs for every branch regardless of whether a pipeline_config.groovy is present or not.
Repository Configuration
Note, the GitHub Organization project can configure a Governance Tier for specifying pipeline templates, library sources, and applying a pipeline configuration to every branch of every repository in a GitHub Organization.
You can find these settings under the Jenkins Templating Engine section of the job configuration.