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Indeed. I realize there's a drive to move to Jgit for git-client, but it's apparently not ready for prime time when it comes to complex filesystems in Unix.
More info on git's "procelain" versus "plumbing" (and the counter-intuitive use of the term porcelain versus the option "--porcelain") can be found here:
http://stackoverflow.com/a/6978402/760905
Since other VCS plugins were switched to pure Java versions, do those plugins handle symlinks and other low-level, OS-dependent features properly? (Of course CVS doesn't know about symlinks to begin with, but SVN certainly does.)