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Linux/Mac OS X
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To install doxygen: 
$sudo apt-get install doxygen

If the above does not work go to:
http://www.stack.nl/~dimitri/doxygen/download.html for the correct download.

Then go to the following website for inforamtion on the install:
http://www.stack.nl/~dimitri/doxygen/install.html

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 unless you chenged the output directory. 

The other option for generating the documentation is to use the wizard:
$doxywizard &

doxywizard information:
http://www.stack.nl/~dimitri/doxygen/doxywizard_usage.html

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Or go to the Doxygen Manual for information at the website noted below.
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Windows
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Go to the following website for the correct download and follow the wizard to install:
http://www.stack.nl/~dimitri/doxygen/download.html

Run the wizard to generate the documentation. 
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Go to the website below or the Doxygen Manual for information on running doxywizard.
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http://www.stack.nl/~dimitri/doxygen/doxywizard_usage.html

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Doxygen Manual
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http://www.stack.nl/~dimitri/doxygen/