Here is a patch of some reorganization of doxygen.  The main changes:
- a new file doc/modules to organize the doxygen by source code module.  This also resulted in a lot of small touches to the source to put "\ingroup" tags to make them subgroups.
- new directory doc/howtos/-- this is intended for lengthier howtos-- it ends up as a "Related Page"
- tutorial is absent from this patch, however (plan to go back to texinfo)
- change main.txt to main.h-- proposal that we use the ".h" suffix consistently for doxygen files

An open issue:
- where does doc/tracing.h live?  Should files of this type be moved to the howtos directory, or to the src/core module itself?