I don't use Civil3D but downloaded the project anyway as it is a nice example of how to automatically create a .bundle file when compiling the code. It also shows how to remove the .bundle file when cleaning the project.
Thanks for the post BlackBox.
I haven't tested this for myself yet, but do be mindful of cleaning any .bundle that includes a .CUIx, as you'll also need to clean the .CUIx, *.MNR (dark), and *_light.MNR files from each-and-every-single version's %AppData%\Autodesk\<Product>\<Release>\<Language>\Support folder as well.
Cheers
[Edit] - To date, I simply have my projects compile debug/release assemblies to %AppData%\Autodesk\ApplicationPlugins\<MyApp>.bundle\Contents\Support\, so when I run from Visual Studio all is loaded at the correct time, without having to manually copy, etc. I'm interested to see if this new mechanism is more useful or not.