Add coordinate-frames.doxygen.md to Doxygen alongside .dox

Update README.md to act as the Doxygen mainpage and include
additional information about the motivation for this project.
Add links from there to Doxygen output .html pages generated
by two files:
 - coordinate-frames.dox (already part of repository)
 - coordinate-frames.doxygen.md (new)

Create coordinate-frames.doxygen.md (Doxygen Markdown format)
file by copying the Jupytext Markdown format output file
coordinate-frames.md and performing a few find and replace
operations:

Find      | Replace
----------|-----------
$$ (start)| \f[
$$ (end)  | \f]
$         | \f$

Surround the jupytext metadata with <!-- --> instead of ---
to comment it out during Doxygen processing.

Doxyfile

@@ -823,7 +823,9 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = coordinate-frames.dox
+INPUT                  = README.md \
+                         coordinate-frames.dox \
+                         coordinate-frames.doxygen.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
@@ -1020,7 +1022,7 @@ 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 = README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -1537,7 +1539,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.

README.md

@@ -1,9 +1,28 @@
-Software used to develop this codebase:
+Attempting to find the best combination of two tools:
+ - Doxygen for overall project documentation
+ - Jupyter Notebook for quick interactive visualizations
+
+Generate the Doxygen `html` documentation package:
+
+    doxygen Doxyfile
+
+Will Jupytext allow us to keep these files in sync?
+
+Synced   | File                         | Description                        | Links to Doxygen Output
+---------|-----------------------------|------------------------------------|---------------
+Manually | coordinate-frames.dox        | Doxygen C-style comment file       | [.html page name](coordinate-frames-dox.html) and [\\ref command](\ref coordinate-frames-dox)
+Manually | coordinate-frames.doxygen.md | Doxygen Markdown format            | [.html page name](md_coordinate-frames_8doxygen.html) and [.md file name](coordinate-frames.doxygen.md)
+Jupytext | coordinate-frames.ipynb      | Jupyter Notebook for interaction   ||
+Jupytext | coordinate-frames.md         | Jupytext (GitHub?) Markdown format ||
+Jupytext | coordinate-frames.py         | Python script                      ||
+
+
+## Dependencies
 
 Software           | Source
 -------------------|----------
 Anaconda 3 2020.02 | [Anaconda3-2020.02-Windows-x86_64.exe](https://repo.anaconda.com/archive/Anaconda3-2020.02-Windows-x86_64.exe)
 Jupytext 1.4.2     | `conda install -c conda-forge jupytext`
 Doxygen 1.8.18     | `conda install -c conda-forge doxygen`
 MikTeX 2.9.6753    | `conda install -c conda-forge MikTeX`
-GhostScript 9.22   | `conda install -c conda-forge GhostScript`
+GhostScript 9.22   | `conda install -c conda-forge GhostScript`

coordinate-frames.dox

@@ -14,7 +14,7 @@ jupyter:
 */
 
 /**
-\mainpage
+\page coordinate-frames-dox
 
 # Vector Nomenclature
 Points in 3D space shall be given unique names: \f$A\f$, \f$B\f$, etc.