This uses a completely new parsing system based on PyParsing (http://pyparsing.wikispaces.com/) but it should be faster and mush more resilient.
If this new dependency is deemed oer the top then PyParsing can probably be directly included in SVN as it is only 1 Python file.
Change the file extension to 'rst' rather than 'txt' to avoid clashes with CMakeLists.txt and to help syntax highlighting.
Add the doxylink Sphinx extension from sphinx-contrib to provide Doxygen links.