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Thanks for your explanations about the JGit implementation, I got it now.
I did some more tests and realized the issue is somehow related to the custom version of Git for Windows that I'm using (mingwGitDevEnv, see [1]). I can confirm that everything is fine if I clone the sandbox repository at [2] (which contains several Linux links) with msysgit 1.8.4 as the plugin's client [3]. But if I configure the plugin to use mingwGitDevEnv it fails cloning like at [4]. However, here comes the funny part: If I just create a build step where I clone the sandbox repository using mingwGitDevEnv manually, i.e. by directly invoking the mingwGitDevEnv Git executable instead of the Jenkins Git plugin doing it, it works again (see [5]). So there must be something that the plugin is doing different than I when calling git.exe for cloning. Any idea what that could be?
[1] https://github.com/sschuberth/mingwGitDevEnv
[2] https://github.com/sschuberth/sandbox
[3] http://mingwgitdevenv.cloudapp.net/view/Playground/job/sandbox/7/console
[4] http://mingwgitdevenv.cloudapp.net/view/Playground/job/sandbox/8/console
[5] http://mingwgitdevenv.cloudapp.net/view/Playground/job/sandbox/9/console