Remove the need for ls-NonFileTypes

[codewithtyler]

Originally documented by @sayedihashimi in ligershark/side-waffle#318

Currently we look through the project file to figure out what files need to be merged with the .vstemplate file. Many project files have items which do not point to files. The current design for this is that we have ls-NonFileTypes to figure out what items to ignore during the .csproj->.vstemplate merge. This has caused issues with new project types.

Instead of this, we should just check for the existence of the file on disk. If the file is not there issue a message and then just ignore it. Then we can just get rid of ls-NonFileTypes.