I've downloaded the big file HTML version of some manuals, and the links in the table of contents frame to the left of the window refer to the LilyPond web site, rather than the local copy. The links in the main text refer to the local copy. This is a bit of a pain if the internet's being slow (or possibly it's the servers), as well as a bit confusing.
Is this meant to happen?
The manuals I've tried are the learning, motation and internals.