Thanks for taking the time to look at the proposals. It seems the opinions are converging. Good!
Nevertheless, I made a last attempt that is in-between 3 and 4: it use the grouping mechanism of 3, but a structure more like 4 where the "-> Reference" link has been replaced by the true reference block with Modules and Classes:
I also tweaked the _javascript_ to enforce the "Chapters" section to be expanded whatsoever. This is probably the most interesting thing about this variant, and the same trick can be applied the #4 one to keep the first level of the User Manual always visible.
If you are only interested by the reference pages, then 4 remains better.
cheers,
gael