I know this is a very broadly scoped question, but what do I need to know to begin creating a branded, custom IDE for course-ware using the VS Shell in isolated mode. Very little useful info on this beast is available through searches, so I'm hoping for some tips and references from gurus that have been through the apparently difficult exercise of using this foundation.
Visual Studio Shell - Creating a Custom IDE
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Here you have a basic example of how to build an isolated shell:
http://msdn.microsoft.com/en-us/library/bb685514.aspx
If you redo the walkthrough you will see how it works. Do this in combination with the examples provided with the Visual Studio SDK and you're on your way.
If you need any help, I will surely help you out.
(If you need examples for Visual Studio 2010 I can help you out aswell).
You can start over here: http://msdn.microsoft.com/en-us/vsx/default.aspx