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I can confirm that updating the timeout resolved the issue for our very large repository. Here's a bit more hand-holding for ubuntu servers.
sudo /etc/init.d/jenkins stop
sudo vi /etc/init.d/jenkins
(insert this directly below DAEMON_ARGS)
#Timeout is in minutes, 120 = 2 hours
JAVA_ARGS="-Dorg.jenkinsci.plugins.gitclient.Git.timeOut=120"
sudo /etc/init.d/jenkins start