[docs] Switch to markdown mainfile

Supported for doxygen 1.8.3 and later (released 2012)

doc/doxygen/Doxyfile

@@ -866,7 +866,8 @@ INPUT                  = src/base \
                          src/transport \
                          src/zeroD \
                          include \
-                         doc/doxygen
+                         doc/doxygen \
+                         doc/doxygen/mainpage.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1027,7 +1028,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = mainpage.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing

doc/doxygen/mainpage.md

@@ -0,0 +1,23 @@
+# %Cantera C++ Reference
+
+Use the menu at the top to view detailed documentation of the code, or use the
+following shortcuts:
+
+* Overview of [**Cantera Modules**](modules.html)
+* Index of [**Cantera Classes**](classes.html)
+
+A topical overview is provided as follows:
+
+* @ref compobj (interface to %Cantera core objects)
+* @ref thermoprops (temperature, pressure, energy, ...)
+* @ref chemkinetics (reactions, rates of progress, reaction path analysis, ...)
+* @ref tranprops (diffusion, viscosity, thermal conductivity, ...)
+* @ref ZeroD (reactors, walls, flow devices, ...)
+* @ref onedim (flames, flow domains, boundaries, ...)
+* @ref physConstants (universal constants, built into %Cantera for convenience)
+
+For fundamental scientific theory used for the implementation of %Cantera, refer to the
+[Cantera Science Section](https://cantera.org/science/index.html) of the
+[Cantera Website](https://cantera.org).
+
+The %Cantera source code is hosted on [GitHub](https://github.com/Cantera/cantera).

include/cantera/base/Solution.h

@@ -17,8 +17,8 @@ class Kinetics;
 class Transport;
 class ExternalHandle;
 
-//! @defgroup compobj Composite Objects
-//! Composite objects create a high-level interface to Cantera's core objects.
+//! @defgroup compobj Objects Representing Phases
+//! High-level interface to %Cantera's core objects.
 
 //! A container class for chemically-reacting solutions.
 /*!

include/cantera/zeroD/ReactorBase.h

@@ -15,9 +15,10 @@ namespace Cantera
 
 //! @defgroup ZeroD Zero-dimensional reactor networks
 //!
-//! See https://cantera.org/science/reactors.html for a description of the governing
-//! equations for specific reactor types and the methods used for solving networks of
-// interconnected reactors.
+//! See the [Reactor Science](https://cantera.org/science/reactors/reactors.html)
+//! section of the %Cantera website for a description of the governing equations for
+//! specific reactor types and the methods used for solving networks of interconnected
+//! reactors.
 
 class FlowDevice;
 class WallBase;