Full D3E uses the Publisher's Toolkit to process HTML files. The toolkit generates a frames-based environment with automatic hyperlinking for navigating around sections, checking citations and footnotes, and tight integration with a discussion space for critiquing documents (see some screenshots and example applications).
The toolkit currently interfaces to two web discussion systems:
Ubiquitous D3E is ideal for quickly setting up a discussion on an interesting URL. It generates a discussion space next to the website, with threads focusing on topics that you specify.