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As I switch our old WebForms projects to leverage publishing, I noticed that only the root web.config files are properly considered for deployment, transformed and copied on publish, while web.config files inside of other folders in the project (used usually for setting Location-based permissions) are completely ignored.
I believe it should be possible to treat these nested web.config files the same way as the root one so that they properly participate in the publishing pipeline.
I've not yet worked around this issue, so suggestions on how to do so besides manually marking each individual file as Content in Visual Studio are welcome.