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I decided to go with both approaches (make the autoconfig for repositories @ConditionalOnMissingBean(RepositoryFactoryBeanSupport), so the first one wins; and also make them conditional on spring.data.*.repositories.enabled=true. The ordering problem is still there really (it's not defined which repositories will be created by the autoconfig), so if a user is going to have 2 repository implementations on the classpath, he is going to have to either choose one to disable, or manualy @Enable* the other one. Fixes gh-1042