When I load a new Unity project or pull source from SCM which uses Noesis I need to set ApplicationResources in the Noesis UI to my application XAML resources. I wanted to ask - is there a good way to set this value programatically? Thanks!

In hindsight.... I realize that instead I should find where this setting is stored and make sure that file is checked into SCM!

Exactly, it is stored in 'Assets\NoesisGUI\Settings\Resource\NoesisSettings.asset'. Make sure you have it in your repository and everything should work fine.