Hello,
I've sucessfully finished building the extended CHM.
About the related bugs: #25363 is fixed, althought #26311 isn't (the _index.php problem).
#29749 is also not fixed. This is related to some JS problems. I think this is a PhpZ skin specific problem, which is totally broken.
I couldn't fix this because I'm not a js expert. If someone could take a look at this...
The final result is avaliable at: http://testes.aborla.net/php_manual_chm_13.zip
Nuno
