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Unfortunately, it is not that the problem is not reproducible. I agree that it is reproducible.
If you haven't seen the problem yet with command line git, then it is probably because you have not started your command line git clone from a deep enough directory structure to show the problem. We saw the problem when we would checkout a Microsoft.Net project with long package names and long file names into a workspace in \users\jenkins\workspace. We ultimately placed our workspaces in C:\J\ to avoid the problem.
The problem is inside the msysgit command line git client. It is not something which can be fixed by changes to the git-client-plugin, other than by replacing all use of the command line git client with calls to JGit. Unfortunately, JGit is not a full-function replacement for command line git yet, and even if it were, the full set of command line workflows are not yet implemented in the JGit portion of git-client-plugin.
The CliGitAPIImpl java class makes a call to the command line git program (git.exe) to fetch and checkout the repository. The "git checkout" command is performed by the git command line client program. That "git checkout" is the place where the limitation is encountered.
You don't need to switch to the JGit implementation with that command line argument. Use the Jenkins global configuration page to add a git implementation and select JGit from the dropdown menu. Then you can use the job configuration menus to switch the individual job to use JGit as well. JGit is becoming more and more capable and may eventually have sufficient functionality to completely supersede command line Git.