Updated the spec to be in line with current policy.

- Adds `manual` field (closes #119)
- Adds `description` and clarifies abstract (closes #223)
- Removes `pre_depends` (closes #226)
- Documents `$vref`
- Clarifies identifier (references #89)
- Clarifies license

Updated code so that it *will* read old documents (including those in
the registry), although it loses github information, as this field has
been deprecated in favour of `repository`.
Updated the NetKAN to generate files according to the new spec.

This is really just a change to how we handle resources.
Merge pull request #253 from pjf/spec_fixes

Updated the spec to be in line with current policy.