I have been over the documentation, http://msdn.microsoft.com/en-us/library/windowsazure/ee460799.aspx and dont see any reference for Azure Websites?
How do visual studio or Webmatrix deploy the site to Azure Websites? an internal API or did I miss the documentation for deploying a Azure Website from Code?
There's a REST API for websites which is used by Visual Studio and CLI tools behind the scenes however it is not publicly available. One thing you could do is take a look at the source code for CLI tools on Github: https://github.com/WindowsAzure/azure-sdk-tools-xplat and figure out the REST API from there.
