After correctly setting up clj-kondo, you might want to leverage its powers during the test / build phase your project.
Since clj-kondo merges configuration files and gives precedence to config files provided explicitly, a useful thing to do when integrating it with your CI workflow is to specify a custom configuration file, such as .clj-kondo/ci-config.edn with CI-specific overrides.
Then put in your pipeline the execution of the tool as
clj-kondo --lint src --config .clj-kondo/ci-config.edn
In this way, you can keep your configuration in the standard config.edn file and that will continue to work during development, with the overrides only be used during CI.
A number of GitHub Actions that use clj-kondo are available: