ToolkitScriptManager and Web Deployment Project

Problem description
If you use AJAX Control Toolkit in your project you probably use ToolkitScriptManager from the Toolkit instead of standard ASP.NET ScriptManager class. Now if you want to deploy your web application using Web Deployment Project (WDP) for VS2008 then you will find out very quickly that your AJAX enabled application features don't work. The reason for that is there is a JavaScript error on a page saying that the root JavaScript object for AJAX Control Toolkit is not defined on the page and all the subsequent scripts relying on that object have failed. I am not reproducing the exact message here because it may vary in different situations.

Background
You have tested your web application many times in your Dev environments and everything worked just fine. So what you've changed is you used a Web Deployment Project to build and deploy your web application and you presumably wanted to take advantage of a famous precompile and merge feature of the WDP.

Explanation
Now the problem is that the missing JavaScript on the page is rendered by a ToolkitScriptManager object that generate a link to a JavaScript code using a ScriptResource handler which is in its turn supposed to retrieve the code embedded into assembly. Because WDP changes the names and locations of the assemblies ToolitScriptManager was unable to resolve the assembly name and could not generate the link so your page does not have that JavaScript reference any more.

Workaround
Use standard ASP.NET ScriptManager instead of ToolkitScriptManager and everything will work again.

What's next?
I am in a process of investigating whether a ToolkitScriptManager brings any advantages comparing to a new ScriptManager 3.5 in terms of more efficient HTML rendering and will post here my findings as soon as possible.

Also if you are interested in employing a ToolkitScriptManager together with the Web Deployment Project I invite you to vote for this bug on Codeplex.