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graft: record intermediate grafts in extras
Previously the extra field for a graft only contained the original commit hash.
This made it impossible to use graft to copy a commit more than once, because
the extras fields did not change after the second graft.
The fix is to add an extra.intermediate-source field that records the immediate
predecessor to graft. This changes hashes for commits that have been grafted
twice, which is why the test was affected.
