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There should be a unified view that links together all records and all tables (all linked records “left joined” automatically, or could be an option of left, right, outer or inner). This way, you could apply features such as roll-ups and counts without needing to update the linked records (“re-linking everything”) every time.
This will allow querying across tables from outside all of them as well…
I realise that there might be issue with recursion, but should be resolved easily by putting a recursion level that should be rendered in the menu or putting a soft cap (or both!)