Today, I talk with Octave Developers at their mailing list and discuss my problem with them. They told me that, Doxygen can’t understands proper style and grammer of .m files. It is useful for another languages. Some developers tried doxygen documentation of m files using script preprocessing. They said that you are welcome to try to get something working, let us know if you have something that others might find useful. But you will be pretty much on your own. They also told me that they are using Texinfo for GNU project documentation. Now I am reading about Texinfo.