Mac OS X
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To install doxygen and dot: 
brew install doxygen dot

doxyqml:
https://github.com/agateau/doxyqml
$sudo pip3 install doxyqml

Then to generate the html, run the following code while you are in the qgroundcontrol/doc directory:
$doxygen Doxyfile

The html file index.html should be in doc/html. 

Debian
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#To build documentation first install dependencies (doxygen, doxyqml and dot):
sudo apt install doxygen graphviz doxyqml

#Then build documentation in the doc/ directory
doxygen ./Doxyfile