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Using a default msysgit installation on multiple Windows machines, I was unable to duplicate this problem with git-client-plugin 1.6.2 and git-plugin 2.0.1. When the checkout is performed on Windows 2011 home server, Windows 7, and Windows 8.1 (in my Jenkins environment) with a symbolic link to a file in the root directory, and with a symbolic link to a directory in the root directory, the checkout is successful.
The Windows based checkout of the symbolic links is not very useful on Windows, but it does not prevent the checkout. Can you provide any further hints that could help with verifying the bug still exists?