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I can't explain why that symlink is necessary though I believe it was/is related to the operation of the puppet module involved (I'm not the direct developer of the code itself). It probably resolves differently on the target system (the symlink is ../../.. and the path apt/spec/fixtures may itself have symlinks involved).
That aside, it's unexpected behavior when a change like this breaks Jenkins even though git itself remains perfectly happy with such symlinks (it took a while to figure out where the problem was occurring so I could get our systems back online). It does appear to be a bug in Jgit, and this transition to Jgit opens Jenkins up to other Jgit bugs as well. What drove this sudden switch away from normal git (which is more robust and feature-rich overall)?
And for all this, it would be useful to have the git-client in the list of plugins: it would have saved a lot of time during the downgrade process.