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Git supports using the same local repository for multiple checked-out worktrees. JGit does not fully support this, so we have to do some workarounds for it to work. The previous workaround provided by diffplug#965 did not take `commondir` into consideration, which is the location of a few files. More details are available at: https://git-scm.com/docs/git-worktree#_details
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