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I believe I've understood now what was causing this behavior: Before JGit 3.3, JGit was not setting the local core.symlinks at all when initializing a repository, which means querying core.symlinks would fall back to the global and system scopes. msysgit sets core.symlinks = false at the system scope, which is why the checkout on Windows did not try to create symlinks in that case and succeeded. mingwGitDevEnv on the other hand does not set core.symlinks at all, so it's unset at all scopes, and the checkout tries to create symlinks, which fails on Windows. My work-around to set core.symlinks = false at the system scope also for mingwGitDevEnv so is exactly what msysgit does out of the box.
With JGit 3.3 the situation has changed in that it now (Always? See JENKINS-22376 and
JENKINS-22391.) sets core.symlinks = false at the local scope, rendering the system scope setting redundant.So this fix to this issue is the same as for JENKINS-22376 and
JENKINS-22391: Use the CLI instead of JGit to initialize the repository.