We have a problem with phpDocumentor in that it crashes when I try to run it with the 1.6 codebase. I don't know if this is fixable or not at present. Since phpDocumentor is hard to maintain anyway we are currently looking at other possibilities, such as Doxygen and trying to figure out if there is a way to merge the output from that tool into the wiki so as to centralise into a single resource instead of having the API Reference split between
api.joomla.org and the wiki. Hopefully we'll have a solution before 1.6 becomes stable ;)
The wiki API Reference at
http://docs.joomla.org/Framework will continue to be updated to cover 1.5, 1.6 and beyond.
Chris.