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I was wrong, or incomplete in my description of the problem. If a repository is initialized by JGit 3.3.0 on JDK 6, it writes core.symlinks=false to the local repository config file. That is correct if the only client used in that repository is JGit. However, if (as was the case before git-client-plugin 1.7.0) JGit were used to initialize the repository, then command line git were used for all other operations, then the config setting was wrong.
The git-client-plugin 1.7.0 fixes that cases of the problem by using command line git to initialize repositories which will use command line git.