If you look at the maps at the beginning you'll see that the tunnel cuts across many streams. Where ever there was a stream there was a bit of open ditch. There are a few reasons for this. One is just geologic. You need a ditch where there is no ground to tunnel through. Two when digging a long tunnel you need places to toss out the rocks blasted away forming the tunnel. Here are a few pictures of the first place we came across the tunnel becoming a ditch.
If you click on the below picture you'll see a bit of the tunnel where it flows into the ditch.
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