As I read the Labs, Microsoft is highly suggesting the use of Master Pages in Atlas applications to simplify the the creation of Atlas applications. What about adding a master page with the necessary stuff in it when an Atlas application is created in the IDE.
WallyThe ScriptManager control works better for generating script references than using shared references stored in a master page.
In my humble opinion, the labs are giving some bad advice. I see master pages being abused in the newsgroups as a container for common code and functionality, which I feel is going to be a maintenance problem later in the app's lifecycle.
http://odetocode.com/Blogs/scott/archive/2005/09/10/2179.aspx
I'd be more comfortable if the common Atlas goo was defined in (or injected from) a base class I derive from Page. If the common goo is really generic enough, perhaps the framework can automatically inject what it needs based on a property we can set before OnInit, e.g. <% @. Page AtlasEnabled="true" ... %>.
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