Fix bug in config set when flag --config is provided

[jlewi]

• config set agent.model wasn't working when you use "--config" to specify a non default config file
• The break occured because of

  foyle/app/pkg/config/config.go

  Line 366 in e03b8fe

  globalV = viper.New()

• That change meant InitViper was no longer operating on the global instance.
• However this line

  foyle/app/cmd/config.go

  Line 60 in e03b8fe

  viper.Set(cfgName, cfgValue)

  which was modifying the configuration was using the global instance
• This PR fixes this by being explicit about the instance of viper used.
• The unittest verifies we correctly modify the configuration

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