Patrick B if your users need to increase the timeout generally, then I think you may have missed an opportunity to help your users with faster clones. Refer to the Jenkins World 2017 15 minute talk on "git in the large" (slides).
For example, cloning a large git repository can be significantly reduced with a reference repository. Cloning a large git repository can be significantly reduced by using a narrow refspec. Cloning a large git repository can be significantly reduced with shallow clone.
Even with the best of techniques, there still may be times when you choose to attempt to adjust the global git client plugin timeout value. That requires a change of the command line parameters used to start Jenkins. There is no user interface support for global adjustment of the git client plugin timeout value.
In general, the Java process which starts Jenkins needs the argument -Dorg.jenkinsci.plugins.gitclient.Git.timeOut=12345
Refer to my docker_run.py script as one example of a way to pass that argument to the java command which starts Jenkins. If your Jenkins starts from an init script on Ubuntu or Debian, you may be able to adjust command line arguments from /etc/defaults/jenkins. If your Jenkins starts from an init script on Red Hat, CentOS, OpenSUSE, or SUSE, you may be able to adjust command line arguments in /etc/sysconfig/jenkins. If your Jenkins is a service on Windows, I believe there is a configuration file that can be changed to add arguments to the Java command line which starts Jenkins.