I need to keep the production app settings section outside of Web.config; I don't want keys and other secret information to be kept inside source code repository. However, if I edit the app settings with IIS Mananger it changes the Web.config, which will be overwritten at the next deployment.
How can I keep those settings outside of the Web.config that comes with the application on deployment? For example, this is somehow done by Azure Web Sites - the app settings you configure in the portal are not stored in Web.config - that can be confirmed by downloading the file via FTP. How is it done?