Xml configuration or Configuration through code?

No matter which particular DI Container you use, you should always defer the resolution of the application's object graph to the last responsible moment . This is called the application's Composition Root .

To answer your question you can have your cake and eat it too in StructureMap. You can configure your container from code and push in that extra bit of config you need from the application configuration. That is what EqualToAppSetting is for.

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