Stop removing non-cookbook files to fix #537

Test Kitchen removes what it considers to be "non-cookbook files" based on its own logic. Ideally, Test Kitchen should follow convention and look at the chefignore file: https://docs.getchef.com/essentials_repository.html#chefignore-files.

This is the root cause of Issue #537.
It is better to delete code stored in git than to comment it out.