Convert list of links to hyperlinks in HTML.

TODO:

- [x] add element IDs to each paragraph (url/page#item.id)
- [x] convert the list of links into hyperlinks
- [x] move publish/export integration tests and use real objects
- [x] move tree publishing/exporting logic from the `cli` to `core`
- [x] only 'linkify" when the whole tree is published as HTML
- [x] only add extended Markdown (IDs, links, etc.) when it's required for HTML
- ~~add a CLI argument to force "linkify"~~
    - There doesn't seem like a common use case. The APIs are available internally.