Reset several Doxygen options to their default values

The goal is to minimize the output of `doxygen -x DOCS/Doxyfile` so that
it contains only the settings specified in CMakeLists.txt.  In all
cases, the changed values are intended to match what CMake is generating
when using -DBUILD_HTML_DOCUMENTATION=ON, and ideally the changes should
have no effect.

Comments for ABBREVIATE_BRIEF and EXAMPLE_PATTERNS describe the default
behavior when they are blank, but our blank values show up in the output
of `doxygen -x DOCS/Doxyfile` indicating that blank is not the default
value.  Setting values to match the current default behavior should have
no effect, unless Doxygen changes in the future.  On the other hand,
MATHJAX_RELPATH has changed and will change again in newer Doxygen
versions.

CMake automatically inserts its own set of EXCLUDE_PATTERNS that
contains none of the patterns previously listed here.  Neither the
previous values nor the CMake-generated ones should have any effect due
to our choice of INPUT and FILE_PATTERNS.

MATHJAX_RELPATH, LATEX_CMD_NAME, RTF_HYPERLINKS, and MAN_LINKS all
require some other option (USE_MATHJAX, GENERATE_LATEX, GENERATE_RTF,
and GENERATE_MAN, respectively) to be set to YES to take effect, and all
are set to NO, so these changes should have no effect.  Note that the
CMake-generated Doxyfile.man sets MAN_LINKS=YES in addition to
GENERATE_MAN=YES.

DOCS/Doxyfile

@@ -126,7 +126,17 @@ REPEAT_BRIEF           = YES
 # the entity):The $name class, The $name widget, The $name file, is, provides,
 # specifies, contains, represents, a, an and the.
 
-ABBREVIATE_BRIEF       =
+ABBREVIATE_BRIEF       = "The $name class" \
+                         "The $name widget" \
+                         "The $name file" \
+                         is \
+                         provides \
+                         specifies \
+                         contains \
+                         represents \
+                         a \
+                         an \
+                         the
 
 # If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
 # doxygen will generate a detailed section even if there is only a brief
@@ -927,11 +937,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = *.py \
-                         *.txt \
-                         *.in \
-                         *.inc \
-                         Makefile
+EXCLUDE_PATTERNS       =
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -955,7 +961,7 @@ EXAMPLE_PATH           =
 # *.h) to filter out the source-files in the directories. If left blank all
 # files are included.
 
-EXAMPLE_PATTERNS       =
+EXAMPLE_PATTERNS       = *
 
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
 # searched for input files to be used with the \include or \dontinclude commands
@@ -1602,7 +1608,7 @@ MATHJAX_FORMAT         = HTML-CSS
 # The default value is: https://cdn.jsdelivr.net/npm/mathjax@2.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
+MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax@2
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example
@@ -1735,7 +1741,7 @@ LATEX_OUTPUT           = latex
 # the output language.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-LATEX_CMD_NAME         = latex
+LATEX_CMD_NAME         =
 
 # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
 # index for LaTeX.
@@ -1938,7 +1944,7 @@ COMPACT_RTF            = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_RTF is set to YES.
 
-RTF_HYPERLINKS         = YES
+RTF_HYPERLINKS         = NO
 
 # Load stylesheet definitions from file. Syntax is similar to doxygen's
 # configuration file, i.e. a series of assignments. You only have to provide
@@ -2009,7 +2015,7 @@ MAN_SUBDIR             =
 # The default value is: NO.
 # This tag requires that the tag GENERATE_MAN is set to YES.
 
-MAN_LINKS              = YES
+MAN_LINKS              = NO
 
 #---------------------------------------------------------------------------
 # Configuration options related to the XML output