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`.

Note: Once we start generating documents using the new spec, old clients will
cease being able to receive updates, and must upgrade. (We're still in
pre-release, so I'm not worried by that.)