Currently, guacenc writes raw mpeg4 frames into a file and gives it a file extension of m4v. While this works for that specific codec and container combination, adding more advanced codecs will require better container support.
FFMpeg provides a library, libavformat, that provides true container support. libavformat should be added as a dependency to guacenc and the current file writing code should be refactored to leverage libavformat. These changes will facilitate future work on adding new codec support to guacenc.