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The git-client-plugin creates a new repository differently than a typical git command line client. It initializes a repository using JGit (creating the .git directory, etc.), and then uses a "git fetch" to bring in the contents from the remote repository.
The specific details of the "git fetch" command will need more time for me to extract them from the source code. I assume that must be the source of the differences between what you observe from the command line and from within Jenkins.
The "git fetch" command is used as a way to reduce the number of cases where a "git" command will hang waiting for interactive authentication.