I've taken your suggestions and incorporated the fixes into the new documentation system here:
All classes and commands are alphabetized, with classes listed first.
All pages in the API Reference should be working now.
If a page does not appear in the old docs, or if a command does not have an example, it will not appear in the new docs, as I am not changing the content right now.
Please let me know if the table of contents of pages have any errors.