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We do not need to reassign metalsmith metadata, because of metalsmith return its internal metadata object. So if something changed in this metadata object its changed for all next plugin.
But when we reassign metalsmith metadata with
metadata(<new metadata>)function this<new metadata>clones with deep copying. And this deep copying breaks the consistency of previously created referencing (for example bymetalsmith-collectionsplugin) from some metadata property to files objects. And if next plugins change something in files, this change will not reflect in metadata, because of metadata property reference to copied files objects.