TODO: Prevent MSBuild from copying these transitive references in the first place

[codespare]

Could the UseCommonOutputDirectory option mentioned on http://blogs.msdn.com/b/kirillosenkov/archive/2015/04/04/using-a-common-intermediate-and-output-directory-for-your-solution.aspx be a solution?

[SLaks]

That won't help.
Just having these DLLs present in the output directory will prevent the application from running, since the CLR loader will bypass by AssemblyResolve handler and load the wrong versions.

Moving the output directory won't change anything.

Thanks, though!