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When looking at the serialization code for LocalMetadataRepository, it appears that whenever we add a site reference, we mark the repo as dirty and re-write the repository. In a lot of cases, the references will be the same across multiple features and as the number of features grow, the problem becomes more apparent. This was noticed in a scenario in which the reconciler was being used to install roughly 2000 features. We should check to make sure that we really did add a new reference before writing out the repository.
Released to HEAD.