Function Reference: Which to use? Where is the link?

Hi. I was looking for the WordPress Function Reference to reinforce my knowledge of the code and I did find it by searching Yahoo as it is not linked to on the Codex main page. Is a link to the Function Reference missing or intentionally not linked to?

http://codex.wordpress.org/Main_Page

Now that I found two references, which one should be used? This one:

http://codex.wordpress.org/Function_Reference

Or this one?

http://phpdoc.wordpress.org/trunk/

I see some functions listed in the PHPDoc reference that I do not find in the WordPress source code files where the reference says it should be. That’s why I have the question.

Thanks.