Fix misc. Doxygen issues

- Fix some missing brief descriptions.
- Fix some function definitions so that Doxygen correctly pairs them
  with the corresponding declarations.
- Fix some documentation visibility issues.  Not all these are strictly
  required, in particular in the SIMD parts, where \cond is used to
  exclude full classes.  But the presence of \cond is
  difficult/expensive to test automatically.
- Also some misc.  other fixes.
- Document some of these issues better on the Doxygen page.
- Exclude parser.h from Doxygen, since it doesn't contain any meaningful
  comments, and confuses Doxygen at least with the XML output.

Also, explicitly list input file extensions for Doxygen.
This excludes some random Python files from the documentation.  At least
for now, we probably want to keep the documentation such that it applies
mainly to the C/C++ code, and not bother how to also document Python
code in a Doxygen-compatible way.
CUDA files are still left out, as they were previously, since they
currently produce several warnings.

Most of these were found by the current work-in-progress checker script.
After these, the checker mainly complains about a lot of missing brief
descriptions in thread-MPI headers and in swapcoords.c.

Change-Id: Ib8a492fde6327ce3d814a23d887b05323bd6d334