How to include config file in WSP?

I don't think this can't be done - I assume for security reasons.

Does NLog. Config need to be a separate file, or can the settings be integrated into the web. Config file?

If you can integrate the settings into the web. Config file, you can add a feature receiver and write the necessary settings during the FeatureActivated or FeatureInstalling event to web. Config using SPWebConfigModifications (just google for it).

You should also make sure to remove the settings in FeatureDeactivating or FeatureUninstalled event.

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