Fix Doxygen build

Docs/Architecture.md

@@ -311,7 +311,7 @@ Because of the minimal use of doubles, the simulation runs 10-20% slower in doub
 
 ## Continuous Collision Detection
 
-Each body has a motion quality setting ([EMotionQuality](@ref EMotionQuality)). By default the motion quality is [Discrete](@ref EMotionQuality::Discrete). This means that at the beginning of each simulation step we will perform collision detection and if no collision is found, the body is free to move according to its velocity. This usually works fine for big or slow moving objects. Fast and small objects can easily 'tunnel' through thin objects because they can completely move through them in a single time step. For these objects there is the motion quality [LinearCast](@ref EMotionQuality::LinearCast). Objects that have this motion quality setting will do the same collision detection at the beginning of the simulation step, but once their new position is known, they will do an additional CastShape to check for any collisions that may have been missed. If this is the case, the object is placed back to where the collision occurred and will remain there until the next time step. This is called 'time stealing' and has the disadvantage that an object may appear to move much slower for a single time step and then speed up again. The alternative, back stepping the entire simulation, is computationally heavy so was not implemented. 
+Each body has a motion quality setting ([EMotionQuality](@ref EMotionQuality)). By default the motion quality is [Discrete](@ref Discrete). This means that at the beginning of each simulation step we will perform collision detection and if no collision is found, the body is free to move according to its velocity. This usually works fine for big or slow moving objects. Fast and small objects can easily 'tunnel' through thin objects because they can completely move through them in a single time step. For these objects there is the motion quality [LinearCast](@ref LinearCast). Objects that have this motion quality setting will do the same collision detection at the beginning of the simulation step, but once their new position is known, they will do an additional CastShape to check for any collisions that may have been missed. If this is the case, the object is placed back to where the collision occurred and will remain there until the next time step. This is called 'time stealing' and has the disadvantage that an object may appear to move much slower for a single time step and then speed up again. The alternative, back stepping the entire simulation, is computationally heavy so was not implemented. 
 
 |![Motion Quality](Images/MotionQuality.jpg)|
 |:-|

Doxyfile

@@ -1,4 +1,4 @@
-# Doxyfile 1.9.3
+# Doxyfile 1.9.5
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -12,6 +12,16 @@
 # For lists, items can also be appended using:
 # TAG += value [value, ...]
 # Values that contain spaces should be placed between quotes (\" \").
+#
+# Note:
+#
+# Use doxygen to compare the used configuration file with the template
+# configuration file:
+# doxygen -x [configFile]
+# Use doxygen to compare the used configuration file with the template
+# configuration file without replacing the environment variables or CMake type
+# replacement variables:
+# doxygen -x_noenv [configFile]
 
 #---------------------------------------------------------------------------
 # Project related configuration options
@@ -60,16 +70,28 @@ PROJECT_LOGO           = ./Docs/LogoSmall.png
 
 OUTPUT_DIRECTORY       = ./Build/Doxygen
 
-# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
-# directories (in 2 levels) under the output directory of each output format and
-# will distribute the generated files over these directories. Enabling this
+# If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
+# sub-directories (in 2 levels) under the output directory of each output format
+# and will distribute the generated files over these directories. Enabling this
 # option can be useful when feeding doxygen a huge amount of source files, where
 # putting all generated files in the same directory would otherwise causes
-# performance problems for the file system.
+# performance problems for the file system. Adapt CREATE_SUBDIRS_LEVEL to
+# control the number of sub-directories.
 # The default value is: NO.
 
 CREATE_SUBDIRS         = NO
 
+# Controls the number of sub-directories that will be created when
+# CREATE_SUBDIRS tag is set to YES. Level 0 represents 16 directories, and every
+# level increment doubles the number of directories, resulting in 4096
+# directories at level 8 which is the default and also the maximum value. The
+# sub-directories are organized in 2 levels, the first level always has a fixed
+# numer of 16 directories.
+# Minimum value: 0, maximum value: 8, default value: 8.
+# This tag requires that the tag CREATE_SUBDIRS is set to YES.
+
+CREATE_SUBDIRS_LEVEL   = 8
+
 # If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
 # characters to appear in the names of generated files. If set to NO, non-ASCII
 # characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
@@ -81,14 +103,14 @@ ALLOW_UNICODE_NAMES    = NO
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all
 # documentation generated by doxygen is written. Doxygen will use this
 # information to generate all constant output in the proper language.
-# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
-# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
-# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
-# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
-# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
-# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
-# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
-# Ukrainian and Vietnamese.
+# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Bulgarian,
+# Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, English
+# (United States), Esperanto, Farsi (Persian), Finnish, French, German, Greek,
+# Hindi, Hungarian, Indonesian, Italian, Japanese, Japanese-en (Japanese with
+# English messages), Korean, Korean-en (Korean with English messages), Latvian,
+# Lithuanian, Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese,
+# Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish,
+# Swedish, Turkish, Ukrainian and Vietnamese.
 # The default value is: English.
 
 OUTPUT_LANGUAGE        = English
@@ -452,7 +474,7 @@ TYPEDEF_HIDES_STRUCT   = NO
 
 LOOKUP_CACHE_SIZE      = 0
 
-# The NUM_PROC_THREADS specifies the number threads doxygen is allowed to use
+# The NUM_PROC_THREADS specifies the number of threads doxygen is allowed to use
 # during processing. When set to 0 doxygen will based this on the number of
 # cores available in the system. You can set it explicitly to a value larger
 # than 0 to get more control over the balance between CPU load and processing
@@ -577,14 +599,15 @@ INTERNAL_DOCS          = NO
 # filesystem is case sensitive (i.e. it supports files in the same directory
 # whose names only differ in casing), the option must be set to YES to properly
 # deal with such files in case they appear in the input. For filesystems that
-# are not case sensitive the option should be be set to NO to properly deal with
+# are not case sensitive the option should be set to NO to properly deal with
 # output files written for symbols that only differ in casing, such as for two
 # classes, one named CLASS and the other named Class, and to also support
 # references to files without having to specify the exact matching casing. On
 # Windows (including Cygwin) and MacOS, users should typically set this option
 # to NO, whereas on Linux or other Unix flavors it should typically be set to
 # YES.
-# The default value is: system dependent.
+# Possible values are: SYSTEM, NO and YES.
+# The default value is: SYSTEM.
 
 CASE_SENSE_NAMES       = NO
 
@@ -851,10 +874,21 @@ WARN_AS_ERROR          = FAIL_ON_WARNINGS
 # and the warning text. Optionally the format may contain $version, which will
 # be replaced by the version of the file (if it could be obtained via
 # FILE_VERSION_FILTER)
+# See also: WARN_LINE_FORMAT
 # The default value is: $file:$line: $text.
 
 WARN_FORMAT            = "$file:$line: $text"
 
+# In the $text part of the WARN_FORMAT command it is possible that a reference
+# to a more specific place is given. To make it easier to jump to this place
+# (outside of doxygen) the user can define a custom "cut" / "paste" string.
+# Example:
+# WARN_LINE_FORMAT = "'vi $file +$line'"
+# See also: WARN_FORMAT
+# The default value is: at line $line of file $file.
+
+WARN_LINE_FORMAT       = "at line $line of file $file"
+
 # The WARN_LOGFILE tag can be used to specify a file to which warning and error
 # messages should be written. If left blank the output is written to standard
 # error (stderr). In case the file specified cannot be opened for writing the
@@ -884,10 +918,21 @@ INPUT                  = ./Jolt \
 # libiconv (or the iconv built into libc) for the transcoding. See the libiconv
 # documentation (see:
 # https://www.gnu.org/software/libiconv/) for the list of possible encodings.
+# See also: INPUT_FILE_ENCODING
 # The default value is: UTF-8.
 
 INPUT_ENCODING         = UTF-8
 
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses The INPUT_FILE_ENCODING tag can be used to specify
+# character encoding on a per file pattern basis. Doxygen will compare the file
+# name with each pattern and apply the encoding instead of the default
+# INPUT_ENCODING) if there is a match. The character encodings are a list of the
+# form: pattern=encoding (like *.php=ISO-8859-1). See cfg_input_encoding
+# "INPUT_ENCODING" for further information on supported encodings.
+
+INPUT_FILE_ENCODING    =
+
 # If the value of the INPUT tag contains directories, you can use the
 # FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
 # *.h) to filter out the source-files in the directories.
@@ -1035,6 +1080,11 @@ IMAGE_PATH             = .
 # code is scanned, but not when the output code is generated. If lines are added
 # or removed, the anchors will not be placed correctly.
 #
+# Note that doxygen will use the data processed and written to standard output
+# for further processing, therefore nothing else, like debug statements or used
+# commands (so in case of a Windows batch file always use @echo OFF), should be
+# written to standard output.
+#
 # Note that for custom extensions or not directly supported extensions you also
 # need to set EXTENSION_MAPPING for the extension otherwise the files are not
 # properly processed by doxygen.
@@ -1076,6 +1126,15 @@ FILTER_SOURCE_PATTERNS =
 
 USE_MDFILE_AS_MAINPAGE = ./Docs/Architecture.md
 
+# The Fortran standard specifies that for fixed formatted Fortran code all
+# characters from position 72 are to be considered as comment. A common
+# extension is to allow longer lines before the automatic comment starts. The
+# setting FORTRAN_COMMENT_AFTER will also make it possible that longer lines can
+# be processed before the automatic comment starts.
+# Minimum value: 7, maximum value: 10000, default value: 72.
+
+FORTRAN_COMMENT_AFTER  = 72
+
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
 #---------------------------------------------------------------------------
@@ -1171,7 +1230,7 @@ VERBATIM_HEADERS       = YES
 # generated with the -Duse_libclang=ON option for CMake.
 # The default value is: NO.
 
-#CLANG_ASSISTED_PARSING = NO
+CLANG_ASSISTED_PARSING = NO
 
 # If the CLANG_ASSISTED_PARSING tag is set to YES and the CLANG_ADD_INC_PATHS
 # tag is set to YES then doxygen will add the directory of each input to the
@@ -1179,7 +1238,7 @@ VERBATIM_HEADERS       = YES
 # The default value is: YES.
 # This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
 
-#CLANG_ADD_INC_PATHS    = YES
+CLANG_ADD_INC_PATHS    = YES
 
 # If clang assisted parsing is enabled you can provide the compiler with command
 # line options that you would normally use when invoking the compiler. Note that
@@ -1187,7 +1246,7 @@ VERBATIM_HEADERS       = YES
 # specified with INPUT and INCLUDE_PATH.
 # This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
 
-#CLANG_OPTIONS          =
+CLANG_OPTIONS          =
 
 # If clang assisted parsing is enabled you can provide the clang parser with the
 # path to the directory containing a file called compile_commands.json. This
@@ -1200,7 +1259,7 @@ VERBATIM_HEADERS       = YES
 # Note: The availability of this option depends on whether or not doxygen was
 # generated with the -Duse_libclang=ON option for CMake.
 
-#CLANG_DATABASE_PATH    =
+CLANG_DATABASE_PATH    =
 
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index
@@ -1310,6 +1369,23 @@ HTML_EXTRA_STYLESHEET  =
 
 HTML_EXTRA_FILES       =
 
+# The HTML_COLORSTYLE tag can be used to specify if the generated HTML output
+# should be rendered with a dark or light theme. Default setting AUTO_LIGHT
+# enables light output unless the user preference is dark output. Other options
+# are DARK to always use dark mode, LIGHT to always use light mode, AUTO_DARK to
+# default to dark mode unless the user prefers light mode, and TOGGLE to let the
+# user toggle between dark and light mode via a button.
+# Possible values are: LIGHT Always generate light output., DARK Always generate
+# dark output., AUTO_LIGHT Automatically set the mode according to the user
+# preference, use light mode if no preference is set (the default)., AUTO_DARK
+# Automatically set the mode according to the user preference, use dark mode if
+# no preference is set. and TOGGLE Allow to user to switch between light and
+# dark mode via a button..
+# The default value is: AUTO_LIGHT.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_COLORSTYLE        = AUTO_LIGHT
+
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to
 # this color. Hue is specified as an angle on a color-wheel, see
@@ -1673,17 +1749,6 @@ HTML_FORMULA_FORMAT    = png
 
 FORMULA_FONTSIZE       = 10
 
-# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are not
-# supported properly for IE 6.0, but are supported on all modern browsers.
-#
-# Note that when changing this option you need to delete any form_*.png files in
-# the HTML output directory before the changes have effect.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-FORMULA_TRANSPARENT    = YES
-
 # The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
 # to create new LaTeX commands to be used in formulas as building blocks. See
 # the section "Including formulas" for details.
@@ -2274,7 +2339,8 @@ SEARCH_INCLUDES        = YES
 
 # The INCLUDE_PATH tag can be used to specify one or more directories that
 # contain include files that are not input files but should be processed by the
-# preprocessor.
+# preprocessor. Note that the INCLUDE_PATH is not recursive, so the setting of
+# RECURSIVE has no effect here.
 # This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
 INCLUDE_PATH           =
@@ -2297,8 +2363,8 @@ INCLUDE_FILE_PATTERNS  =
 
 PREDEFINED             = _WIN32 \
                          JPH_PROFILE_ENABLED \
-						 JPH_DEBUG_RENDERER \
-						 JPH_PLATFORM_DOXYGEN
+                         JPH_DEBUG_RENDERER \
+                         JPH_PLATFORM_DOXYGEN
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The
@@ -2401,26 +2467,38 @@ HAVE_DOT               = NO
 
 DOT_NUM_THREADS        = 0
 
-# When you want a differently looking font in the dot files that doxygen
-# generates you can specify the font name using DOT_FONTNAME. You need to make
-# sure dot is able to find the font, which can be done by putting it in a
-# standard location or by setting the DOTFONTPATH environment variable or by
-# setting DOT_FONTPATH to the directory containing the font.
-# The default value is: Helvetica.
+# DOT_COMMON_ATTR is common attributes for nodes, edges and labels of
+# subgraphs. When you want a differently looking font in the dot files that
+# doxygen generates you can specify fontname, fontcolor and fontsize attributes.
+# For details please see <a href=https://graphviz.org/doc/info/attrs.html>Node,
+# Edge and Graph Attributes specification</a> You need to make sure dot is able
+# to find the font, which can be done by putting it in a standard location or by
+# setting the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
+# directory containing the font. Default graphviz fontsize is 14.
+# The default value is: fontname=Helvetica,fontsize=10.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+DOT_COMMON_ATTR        = "fontname=Helvetica,fontsize=10"
+
+# DOT_EDGE_ATTR is concatenated with DOT_COMMON_ATTR. For elegant style you can
+# add 'arrowhead=open, arrowtail=open, arrowsize=0.5'. <a
+# href=https://graphviz.org/doc/info/arrows.html>Complete documentation about
+# arrows shapes.</a>
+# The default value is: labelfontname=Helvetica,labelfontsize=10.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_FONTNAME           = Helvetica
+DOT_EDGE_ATTR          = "labelfontname=Helvetica,labelfontsize=10"
 
-# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
-# dot graphs.
-# Minimum value: 4, maximum value: 24, default value: 10.
+# DOT_NODE_ATTR is concatenated with DOT_COMMON_ATTR. For view without boxes
+# around nodes set 'shape=plain' or 'shape=plaintext' <a
+# href=https://www.graphviz.org/doc/info/shapes.html>Shapes specification</a>
+# The default value is: shape=box,height=0.2,width=0.4.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_FONTSIZE           = 10
+DOT_NODE_ATTR          = "shape=box,height=0.2,width=0.4"
 
-# By default doxygen will tell dot to use the default font as specified with
-# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
-# the path where dot can find it using this tag.
+# You can set the path where dot can find font specified with fontname in
+# DOT_COMMON_ATTR and others dot attributes.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_FONTPATH           =
@@ -2446,7 +2524,8 @@ CLASS_GRAPH            = YES
 COLLABORATION_GRAPH    = YES
 
 # If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
-# groups, showing the direct groups dependencies.
+# groups, showing the direct groups dependencies. See also the chapter Grouping
+# in the manual.
 # The default value is: YES.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
@@ -2662,18 +2741,6 @@ DOT_GRAPH_MAX_NODES    = 50
 
 MAX_DOT_GRAPH_DEPTH    = 0
 
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not seem
-# to support this out of the box.
-#
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_TRANSPARENT        = NO
-
 # Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
 # files in one run (i.e. multiple -o and -T options on the command line). This
 # makes dot run faster, but since only newer versions of dot (>1.8.10) support