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Create indexes and files containing these indexes for ee2 queries #413

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@bio-boris

I'd just set them up in MongoUtil. That's more or less how I do it for all my servers, for example https://github.com/kbase/groups/blob/master/src/us/kbase/groups/storage/mongo/MongoGroupsStorage.java#L334-L356

Originally posted by @MrCreosote in #412 (comment)

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