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Per http://stackoverflow.com/questions/18458608/how-to-do-sparse-checkout-in-git-using-java , JGit does not support sparse checkout. I reviewed the pre-release source code for JGit 3.3.0 and found no indication of support for sparse checkout.
That does not preclude implementing sparse checkout in the plugin for command line git, but it would be another case where the JGit implementation does not match the command line implementation.