For some reason doxygen commands like \file and \endcode in example
code fragments break doxygen formatting. Swapped these for /file which
might be a little missleading, but better than broken.

The \file structure commands should be on a line of their own, as now
supported by the new version of tidyc. I also re-ran tidyc over
everything.

Remove other \typedef, \struct, etc doxygen structure commands which
are not needed for comments immediately before the structure.

Fix a few doxygen warnings about missing \param entries for some
functions. Minor improvements to some doxygen comments.

Running 'make doc' is now completely clean and warning free.