I found it. You've got certain theme-related aspects hard-coded in the /App_Start/ BundleConfig.cs.

The bigger question is why isn't everything theme-related in a specific theme?

The way you've got this built now, all themes in the store are forced to use the same version of bootstrap (along with several other libraries). If I want to leverage a newer flavor of bootstrap in a new theme design, I can't do that without impacting all other themes, including the current theme the live store may already be using.

I haven't tried it yet but I sure was thinking about :)

I'll give it a shot this week and let you know.

In my mind, the site is unusable without at least 1 theme, right? You must have at least 1 theme to render the site well enough to edit it. So having the bundle separate doesn't really help much since you still must have a theme to support rendering the site. So we might as well relocate the core bundle list into the default theme for the reasons stated above.

Probably wouldn't hurt to have a dev page explaining the base minimum includes necessary by Able to build a new theme. Sure, people should be building a new theme based on a copy of Sample. But not everyone will do that. In fact, we really need to emphasize to use the Copy feature in the admin themes page. Because if you don't use that copy feature, the path names don't get updated to reflect the new theme in the default view/style files. Kinda learned that one the hard way myself...