Drupal requires its source documentation to be compatible with DoxyGen. If you are working on a large project, you want to install DoxyGen and run it on cron to have nice, up-to-date API docs.

Unfortunatley, if you install Doxygen via yum (or any other auto-updater, I assume) it installs a fairly old 1.4.x branch that is incompatible with Drupal. Specifically, it completely ignores the .module and .install files and has poor support for .inc, from what I can tell. That's because Doxygen does not realize these are PHP source files.

What you want to do is to install the latest Doxygen release (1.5.8 at the time of this writing). In the new version, the author of Doxygen has generously added a configuration tag that allows mapping of arbitrary file extensions with language types. The setting you need in your doxygen configuration file is:

EXTENSION_MAPPING      = module=PHP install=PHP inc=PHP