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I've documented my code for doxygen, but I don't want the default HTML it gives. I know I can customize it by providing custom CSS, headers, footers, etc. (like GNOME does), and how I can add common PHP code to the files and tell it to save as .php, but that isn't really what I want.

What I want is output like MSDN. I can't describe it really. My question is, Is this possible using doxygen with something like templates, or do I have to output XML and parse it with another program (that I wouldn't mind writing)?

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Doxygen does not support something like HTML templates out of the box, as far as I know. You can refer to the image below (from the official doxygen homepage). It shows the input and output files that are related into the entire documentation creation workflow.

enter image description here

As you can see, doxygen reads a so called "Layout file". This file can be customized! However you are somehow restricted to the page structure, doxygen creates.

If you need more flexibility you should prefer to XSLT transform XML output. There is also an sample that shows you how to do this.

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