Philip O'Gorman Please don't create a new issue until you've explored the question on the Jenkins users mailing list or on the chat channel. The stack trace that you've provided is a strong indication that the problem is specific to your environment. Environment specific questions are best handled in the mailing list or in the chat channels where many more people are watching and many more people are helping.
A bug report only gets the attention of the plugin maintainer. A discussion on the mailing list or in one of the chat channels allows many people that are not maintainers to assist with the question.
For example, in your case, it could be as simple as your repository having grown so large that it needs a longer timeout to complete the clone. It could also be that the workspace has existed for a long enough time with enough incremental updates that it needs a garbage collection from git gc.