I don't understand your comment. The method that I describe only requires that the programming language ignores unused files. As far as I know, all modern programming languages have this feature.
The worst is when you move a bunch of files around in Solution Explorer and commit, maybe do a merge and push, before you realise the MSBuild/csproj files were never saved (gotta press Save All for some reason) - now you have a change you need to apply to a pre-merge commit. Good luck with that.
