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You document your source code with special documentation blocks (see section Special comment blocks).
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You generate a configuration file (see section Configuration) by calling doxygen with the -g option:
doxygen -g <config_file>
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You edit the configuration file so it matches your project. In the configuration file you can specify the input files and a lot of optional information.
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You let doxygen generate the documentation, based on the settings in the configuration file:
doxygen <config_file>
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