I created a new ASP.NET Web Forms Project through Visual Studio 2012. Unfortunately, the default Site.Master file is very confusing. (I am posting these questions together
Just to clarify something from the accept answer explanation for Question 1:
The reason for the script references for the individual web forms js files is to allow the local files (such as "~/Scripts/WebForms/WebForms.js") to override the same files that exist in the System.Web.dll (If you reflect the System.Web.dll and look in the references folder you will find the same .js files).