I have not changed manual.xml.in yet, since I beleive it is only viable if we review the structure and selected IDs at least (so notes can be moved and links can be corrected within the manual).
The on-line manual takes so long to update that you can change the manual.xml.in and then we have two months before the content goes on-line :)
Ehem, this is still not the right solution.
But first someone need to correct the huge problem with notes. AFAIK, the Jakub's patch wasn't applied yet (or the master server hasn't updated the CVS...) so we can't move notes.
I have not applied Jakub's patch yet, as it was uncertain to me, what is the position of him on it (it was not clean code, but the user-notes.php file itself is quite ugly: depends on register_globals and magic_qutes_gpc being on).
Goba