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Sounds like you are looking for a data catalog tool instead of db schema management tool. You can check out Amundsen (https://www.amundsen.io/), DataHub (https://datahubproject.io/)
If you are looking for schema change management tool, then you can check out Bytebase (bytebase.com). But it can't answer questions like "which collections contain links to bigmongo.user.id?"
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.
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