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In ecosystems where the dep-graph contains pruned nodes, the dep-graph library functions like pkgPathsToRoot and countPathsToRoot can safely ignore those pruned nodes.
This is because there should be a path to a non-pruned node, the effective path.
Ignoring pruned paths has a number of advantages. Consuming applications are presented with less paths to traverse when operating over paths. When displaying dep-graph path information there is less noise as only the effective paths are shown.