Post leeched in full from my forum posting: http://forums.arcgis.com/threads/6364-Access-Application-Configuration-Manager-Settings-from-.NET-AP...
I'm working on a project where we are customizing / configuring ArcGIS Explorer from both the options available in the Application Configuration Manager and the items available in the Application, Data, Geometry, Mapping and Threading namespaces.
What I don't see from with the API documentation or spelunking into the object models with Reflector is a way to get at the items in the Application Configuration Manager from the .NET API (from a library perspective and not holding a reference to the ApplicationConfigurationManager.exe). In particular, the splash screen, map logo and creation of tab/groups etc on the Ribbon Toolbar.
I do see that the .ncfg file is just a compressed archive with items such as addins, basemaps, images, connections.xml, e3config.xml and e3config.xsd but that seems like a lot of reverse engineering on the consumers end to get to that information.
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