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Switch migrations to use Repository as appropriate
In order for the _updated_at field to be correctly applied the migrations that operate on buckets need to be using the Repository class to modify the data in mongodb. The Repository find() method had to be modified to be able to use both classes that provide a to_mongo_query() method (the Query class) or a Dictionary as would be usual with a mongodb find. I have added some tests to make sure that Repository will work correctly when accepting both types of find() argument.
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