I haven't tried this, but since your Base Page class is in the App_Code folder, this should be easy. Information in App_Code is compiled into the application, you don't even need to a path name, just the class the master page will inherit from. I found a couple pages that include (among many other things) information about the syntax for assigning base classes to Master pages. HTH
http://www.odetocode.com/articles/450.aspx
http://msdn.microsoft.com/en-us/library/c8y19k6h.aspx
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