fix typos
Tweak error messages and related code

* I found the distinction between "project root" and "application root" a
  bit confusing, so tried to make that clearer.

* Addded a test. The Gemfile one is hard to test because there is a Gemfile
  upstream of the test application (the Gemfile for spring itself).

* Moved Spring.verify_environment! to the Run command so that e.g.
  `spring help` works on its own.