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At Notre Dame, we have implemented Nested Collections and leveraged the following indexing strategy:
Nested collections can create infinite loops (e.g. A is in B is in C is in A). At Notre Dame we adopted a maximum depth (aka time_to_live) in graph traversal (another option is Cycle detection but that might not be performant). Also with nested collections, reindexing everything can take considerable time. Those tasks should be relegated to background jobs.