Paths are converted to resource links

Also, moved util funcs into util module

Lists of files are converted, as well as 'ref' keys in the data.
Spec usage of 'ref' is to have an object with that single key and the
value to be the path to a resource.

Example:

subject:
  ref: subjects/cisc

Converts to

subject: http://my_host_name/subjects/cisc