I having kind of absurd situation and I will glad to hear how exactly you guys handling it:
I have a Hybrid App project, Visual Studio 2015 Cordova Tools. Inside it,
For me, the directory that the error message pointed to was just plain missing. Same IDE, same type of app.
It was looking for \GitHub...\myProjectName\platforms\windows\www
I manually added the dir (www) back in and the project ran fine. The IDE deletes that dir at the beginning of the build then throws the EPERM exception. Sure looks like a bug to me.