Manual-Generator with LaTeX or others

I am looking for a way to automatically create nice looking program documentation.
That means information about cross reference, a certain pgm is a) used by ....pgms b) is using...objects c) the structure of pgm is .... (which procedures...) d) fields used in a pgm ...
Task is not to retrieve those information, i will provide xml or other needed input file to produce it.
What i looking for i is something that is able to create manual with flowcharts that show structure and output pdf with hyperlinks...
I think LaTeX is good for that, but open for others too.
Java based approaches prefered.