Adds massive cargo ships to the game, that function similarly to trains. Also adds deep sea oil, oil platforms, tanker ships, train bridges and other water based content.
So basically, there is a possibility to connect waterways and rails. You can place bridge between waterway and rails, and it connects them, allowing train to get onto a waterway and ship to get onto rails.
As far as I know, there is nothing that can be done about it because you can't tell rolling stock to ignore certain rail prototypes (technically, the waterways are rails, and the ships + boats on waterways are based on train prototypes).
Ah, yes. The logic checks to make sure waterways and rails are placed next to the correct bridge side, but doesn't check anything when the bridge itself is placed. I'll see if that's a simple fix or something to be left well enough along. Edit: Yes it's annoying. I'll open a bug on github and maybe get to it eventually.
