First, I like the new SQL Doc (3), it has a lot of nice features. I think there may be a slight problem with the HTML generation. I thought I was just not understanding something but some thought has led me to think it might just be a detail that was overlooked.
When the documentation is generated, it makes 3 .html files in the primary directory:
By default a web browser will request index.html from a URL if no file is specified but the index.html file doesn't have any links. It looks like it is the "splash" page and sure enough, if you load main.html, it appears that tree.html is loaded on the left frame and index.html is loaded on the right frame.
This isn't the end of the world once you figure out what is going on but if I upload my documentation to a server, say mywebserver.com under the web path /databasedocumentation and then open a web browser to http://mywebserver.com/databasedocumentation -- I essentially get a page that does nothing and has no documentation info. I think maybe that what is being put into main.html should be in index.html and vice versa.