when creating the doxyfile.txt for your project, if you want to add (for example) .cl files as input, you might need to make the addition in two places. first to tell it to look for these types of files and the second is how you want these files treated when parsing the marked up file: EXTENSION_MAPPING as well as FILE_PATTERNS variable. Also don't forget to point the OUTPUT_DIRECTORY and INPUT to the appropriate locations.
EXTENSION_MAPPING = cl=C
and add this to FILE_PATTERNS = blah blah \ *.cl
Your file won't be parsed if you don't add this to the top of the .cl file (self referential statement):
/*! \file blah.cl
\brief A test file class.
A more detailed class description.
Running Doxygen (basics):
To run doxygen (assuming it has been added to your path) you can traverse to the directory that the template you generated lives (doxyfile.txt) and it will grab the template. Not recommending this for production but just for getting things up and running.