Even if you let doctrine set indices on FKs in your db or you set indices manually, you still need to add indices in entity files. If you don't know how to have indices on entity files, after doctrine set indices on FKs in your db or you did set them manually to avoid hashed-names, backup your entity files and generate new entity files via console, look at files and you'll see how indices are in entity files, then add them in your actual entity files you did backup before.
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