Fix more Doxygen warnings.

Fix more Doxygen warnings.

- Add documentation for some partially documented classes.
- Some fixes to cosmetic issues in surrounding code that were noticed.
- Some other clean-up.

There are a few warnings in pre-5.0 C code that are not addressed here.
Of the remaining warnings, quite a few are are either in obsolete code
(template.c, displacement.c), or in code that should be heavily
refactored (nbsearch.h, issue #866).

Change-Id: I7c309153769f35e93c4d0ff28667663e6a9e8ee3