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Separate pass to convert hidden nodes into identity nodes - #4644
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Closes #4631. Thanks to @YohYamasaki for reporting and bisecting the issue.
Previously the hidden nodes were dealt with at the same time as the flattening. This meant that there were some cases where e.g. the cloned node wouldn't be added for values when hiding nodes. By separating the passes, the logic becomes more easy to reason about and more robust.
Also added some tests for hidden nodes.