Fixes to avoid errors when running doxygen on source

- This removes all errors and warnings that appear in doxygen.log except
  for warnings about undocumented variables.
- Removed repeated re-use of the same label "section_gridlayout".
- Fixed conflict between sphinx and doxygen for references. Trailing underscore
  is a reference in sphinx.
- Corrected indentation of bullets in MOM_ice_shelf.F90. sphinx complained!
- Documented CPP macros in MOM_memory.h and MOM_memory_macros.h.
- Added section in MOM_thickness_diffuse.F90 to fix sub-section error.
- Removed string "Adcroft's" from MOM_kappa_shear.F90 which for some
  reason was causing the preprocessor in doxygen to miscount #ifdef's!!!
- Added some todo's for missing references.
- Fixed numerous spelling errors.
- Revised Doxyfile configurations for both pure doxygen (github.io)
  and readthdocs.
- Removed api/todo.rst since it wasn't being used.
- Removed tutorial.rst since the MOM6-examples wiki now has a list.
- Added front_page.md for github.io.
- Removed unused .html files from config_src/*.

config_src/dynamic_symmetric/MOM_memory.h

@@ -1,48 +1,33 @@
-!********+*********+*********+*********+*********+*********+*********+*
-!*   This include file determines the compile-time memory settings    *
-!*  for the Modular Ocean Model (MOM), versions 6 and later.          *
-!********+*********+*********+*********+*********+*********+*********+*
+!/*! \brief Compile-time memory settings */
+!/*! \details This include file determines the compile-time memory settings. There are several variants of this file and only one should be in the search path for compilation. */
+!/*! \file MOM_memory.h */
 
-!  Specify the numerical domain.
+!/*! The number of thickness grid points in the i-direction of the global domain. */
 #define NIGLOBAL_ NONSENSE_NIGLOBAL
+!/*! The number of thickness grid points in the j-direction of the global domain. */
 #define NJGLOBAL_ NONSENSE_NJGLOBAL
-                               !    NIGLOBAL_ and NJGLOBAL_ are the number of thickness
-                               !  grid points in the zonal and meridional
-                               !  directions of the physical domain.
+!/*! The number of layers in the vertical direction. */
 #define NK_ NONSENSE_NK
-                               !    The number of layers.
 
+!/*! \def STATIC_MEMORY_ If STATIC_MEMORY_ is defined, the principle variables will have sizes that are statically determined at compile time. Otherwise the sizes are not determined until run time. */
 #undef STATIC_MEMORY_
-                               !    If STATIC_MEMORY_ is defined, the principle
-                               !  variables will have sizes that are statically
-                               !  determined at compile time.  Otherwise the
-                               !  sizes are not determined until run time. The
-                               !  STATIC option is substantially faster, but
-                               !  does not allow the PE count to be changed at
-                               !  run time.
+
+!/*! If SYMMETRIC_MEMORY_ is defined, the velocity point data domain includes every face of the thickness points. In other words, some arrays are larger than others, depending on where they are on the staggered grid. */
 #define SYMMETRIC_MEMORY_
-                               !    If defined, the velocity point data domain
-                               !  includes every face of the thickness points.
-                               !  In other words, some arrays are larger than
-                               !  others, depending on where they are on the 
-                               !  staggered grid.
 
+!/*! The number of processors in the i-direction. */
 #define NIPROC_ NONSENSE_NIPROC
-                               !    NIPROC_ is the number of processors in the
-                               !  x-direction.
+
+!/*! The number of processors in the j-direction. */
 #define NJPROC_ NONSENSE_NJPROC
-                               !    NJPROC_ is the number of processors in the
-                               !  y-direction.
 
+!/*! The maximum permitted number (each) of restart variables, time derivatives, etc. This is mostly used for the size of pointer arrays, so it should be set generously. */
 #define MAX_FIELDS_ 50
-                               !    The maximum permitted number (each) of
-                               !  restart variables, time derivatives, etc.
-                               !  This is mostly used for the size of pointer
-                               !  arrays, so it should be set generously.
 
+!/*! The number of memory halo cells on each side of the computational domain in the i-direction */
 #define NIHALO_ 2
+
+!/*! The number of memory halo cells on each side of the computational domain in the j-direction */
 #define NJHALO_ 2
-                               !   NIHALO_ and NJHALO_ are the sizes of the
-                               ! memory halos on each side.
 
 #include <MOM_memory_macros.h>