Paths are URIs

This pull request should correct the remaining critical errors that appear when attempting to build documentation on Windows systems.

- Revert #29 because it only addressed `CalabashHelper.run`, and other path problems arise for other transformations. This pull request is a more consistent solution to the entire situation.
- Consistently treat paths as URIs for the transformations.
- No need for the transformation templates to add `file:///` to the beginning of a path, because it's already a URI.