Patch to parts/doxygen part2

[Amilcar do Carmo Lucas]

Hi!

I got no answer from the previous patches I sent. :(
But I did some changes to the code meanwhile. :)

So here is the very latest version:
- It updates Doxygen to v1.3-rc3
- It includes the patch from Jens Zurheide to auto compile the 
documentation index

The only problem is that I still couldn't smash bug #51331 :(

-- 
Amilcar Lucas


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