Publish the Web API means to produce a compiled app that can be hosted by a server. Deploy the Web API means to move the published app to a hosting system.
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If you use the Web Deploy method in SnapDevelop, you can directly publish and deploy the Web API to the IIS site folder on the IIS server (the Physical path to the site in IIS Manager).
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If you use the File System method in SnapDevelop, you will publish the Web API to a folder first and then move the folder's content to the IIS site folder on the IIS server.
