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The message "JGit doesn't support reference repository" appears because you've added an advanced configuration option (Advanced clone behaviours) and assigned a value to the reference repository field.
However, that message should not prevent checkout of any arbitrary branch with JGit. It doesn't prevent checkout in the tests I performed.
I created a git repository https://github.com/MarkEWaite/longpaths.git with 4 branches
I defined the job to use JGit, only execute on windows, and to execute a windows batch command: