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This is not a new breaking change but it was not properly documented for the 4.0.0 release.
All nodes in v4 must have unique IDs. This means that manually added passthrough nodes can't have the same ID as their target. The editor should handle this migration better now. Refer to the migration guide for YAML configs.
Bug Fixes
#334: passthroughs are first-class link-graph nodes with unique ids (2415480)
#335: default v4 node type to entity so statistics are fetched (3833841)