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Setting nested viper values leads to config overwriting

Currently viper.WriteConfig() overwrites part of the config when setting a nested value. The overwrite is seemingly random and probably has to do with the new values being held in the override slot of viper. I worked around this issue by unmarshalling the entire repos section of the config, adding the new repo, and writing the entire repos configuration to the config file.

The new LocalRepo should be set with viper.Set(fmt.Sprintf("repos.%s.%s.%s", repo.Remote, repo.User, repo.Name), repo and written to the config with viper.WriteConfig().

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