Upon upgrading to the newest version (4.0.88), I found that Web.Debug.config/Web.Release.config were showing up as items with a ContentType of None in my project despite them not existing on disk:

In addition to showing in Solution Explorer, they also get added as pending changes to TFVC. (Probably not an issue with Git.)

I assume this was added by #44. I tried fixing the SDK but couldn't figure out the correct MSBuild incantation to add an Exclude attribute.

As a workaround I have explicit Remove items in my .csproj for them.