Updated to Doxy 1.8.0.

DOXYGEN IS AWESOME.

config.doxy

@@ -1,4 +1,4 @@
-# Doxyfile 1.7.5.1
+# Doxyfile 1.8.0
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -207,6 +207,13 @@ ALIASES                = "depends=\par Depends on \n"\
                          "expectedException=\par Expects exception:\n" \
                          "group=\par Test Group:\n"
 
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding
+# "class=itcl::class" will allow you to use the command class in the
+# itcl::class meaning.
+
+TCL_SUBST              =
+
 # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
 # sources only. Doxygen will then generate output that is more tailored for C.
 # For instance, some of the names that are used will be different. The list
@@ -245,6 +252,15 @@ OPTIMIZE_OUTPUT_VHDL   = NO
 
 EXTENSION_MAPPING      =
 
+# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
+# comments according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you
+# can mix doxygen, HTML, and XML commands with Markdown formatting.
+# Disable only in case of backward compatibilities issues.
+
+MARKDOWN_SUPPORT       = YES
+
 # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
 # to include (a tag file for) the STL sources as input, then you should
 # set this tag to YES in order to let doxygen match functions declarations and
@@ -327,10 +343,21 @@ TYPEDEF_HIDES_STRUCT   = NO
 # a logarithmic scale so increasing the size by one will roughly double the
 # memory usage. The cache size is given by this formula:
 # 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols
+# corresponding to a cache size of 2^16 = 65536 symbols.
 
 SYMBOL_CACHE_SIZE      = 0
 
+# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
+# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
+# their name and scope. Since this can be an expensive process and often the
+# same symbol appear multiple times in the code, doxygen keeps a cache of
+# pre-resolved symbols. If the cache is too small doxygen will become slower.
+# If the cache is too large, memory is wasted. The cache size is given by this
+# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+LOOKUP_CACHE_SIZE      = 0
+
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -347,6 +374,10 @@ EXTRACT_ALL            = YES
 
 EXTRACT_PRIVATE        = NO
 
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal scope will be included in the documentation.
+
+EXTRACT_PACKAGE        = NO
+
 # If the EXTRACT_STATIC tag is set to YES all static members of a file
 # will be included in the documentation.
 
@@ -420,8 +451,6 @@ CASE_SENSE_NAMES       = NO
 # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
 # will show members with their full class and namespace scopes in the
 # documentation. If set to YES the scope will be hidden.
-# MPB: Turning this to NO will change the classlist to show fully
-# qualified class names, which is sorta ugly in PHP.
 
 HIDE_SCOPE_NAMES       = YES
 
@@ -579,7 +608,8 @@ LAYOUT_FILE            =
 # .bib extension is automatically appended if omitted. Using this command
 # requires the bibtex tool to be installed. See also
 # http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
-# of the bibliography can be controlled using LATEX_BIB_STYLE.
+# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
+# feature you need bibtex and perl available in the search path.
 
 CITE_BIB_FILES         =
 
@@ -665,7 +695,8 @@ INPUT_ENCODING         = UTF-8
 # *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
 # *.f90 *.f *.for *.vhd *.vhdl
 
-FILE_PATTERNS          = *.php *.md
+FILE_PATTERNS          = *.php \
+                         *.md
 
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories
 # should be searched for input files as well. Possible values are YES and NO.
@@ -673,17 +704,18 @@ FILE_PATTERNS          = *.php *.md
 
 RECURSIVE              = YES
 
-# The EXCLUDE tag can be used to specify files and/or directories that should
+# The EXCLUDE tag can be used to specify files and/or directories that should be
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
-# Note that relative paths are relative to directory from which doxygen is run.
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
 
 EXCLUDE                = ./bin/build \
                          ./doc/api \
                          ./dist \
                          .git
 
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
 # from the input.
 
@@ -709,7 +741,8 @@ EXCLUDE_SYMBOLS        =
 # directories that contain example code fragments that are included (see
 # the \include command).
 
-EXAMPLE_PATH           = ./examples
+EXAMPLE_PATH           = ./examples \
+                         docs
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
@@ -872,7 +905,7 @@ HTML_FILE_EXTENSION    = .html
 # standard header. Note that when using a custom header you are responsible
 #  for the proper inclusion of any scripts and style sheets that doxygen
 # needs, which is dependent on the configuration options used.
-# It is adviced to generate a default header using "doxygen -w html
+# It is advised to generate a default header using "doxygen -w html
 # header.html footer.html stylesheet.css YourConfigFile" and then modify
 # that header. Note that the header is subject to change so you typically
 # have to redo this when upgrading to a newer version of doxygen or when
@@ -1100,19 +1133,14 @@ GENERATE_ECLIPSEHELP   = NO
 
 ECLIPSE_DOC_ID         = org.doxygen.Project
 
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
-# top of each HTML page. The value NO (the default) enables the index and
+# at top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it.
+# the value YES disables it. Since the tabs have the same information as the
+# navigation tree you can set this option to NO if you already set
+# GENERATE_TREEVIEW to YES.
 
 DISABLE_INDEX          = NO
 
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
-# (range [0,1..20]) that doxygen will group on one line in the generated HTML
-# documentation. Note that a value of 0 will completely suppress the enum
-# values from appearing in the overview section.
-
-ENUM_VALUES_PER_LINE   = 4
-
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
 # If the tag value is set to YES, a side panel will be generated
@@ -1120,9 +1148,18 @@ ENUM_VALUES_PER_LINE   = 4
 # is generated for HTML Help). For this to work a browser that supports
 # JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
 # Windows users are probably better off using the HTML help feature.
+# Since the tree basically has the same information as the tab index you
+# could consider to set DISABLE_INDEX to NO when enabling this option.
 
 GENERATE_TREEVIEW      = YES
 
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
+# (range [0,1..20]) that doxygen will group on one line in the generated HTML
+# documentation. Note that a value of 0 will completely suppress the enum
+# values from appearing in the overview section.
+
+ENUM_VALUES_PER_LINE   = 4
+
 # By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
 # and Class Hierarchy pages using a tree view instead of an ordered list.
 
@@ -1159,7 +1196,7 @@ FORMULA_TRANSPARENT    = YES
 # (see http://www.mathjax.org) which uses client side Javascript for the
 # rendering instead of using prerendered bitmaps. Use this if you do not
 # have LaTeX installed or if you want to formulas look prettier in the HTML
-# output. When enabled you also need to install MathJax separately and
+# output. When enabled you may also need to install MathJax separately and
 # configure the path to it using the MATHJAX_RELPATH option.
 
 USE_MATHJAX            = NO
@@ -1168,10 +1205,11 @@ USE_MATHJAX            = NO
 # HTML output directory using the MATHJAX_RELPATH option. The destination
 # directory should contain the MathJax.js script. For instance, if the mathjax
 # directory is located at the same level as the HTML output directory, then
-# MATHJAX_RELPATH should be ../mathjax. The default value points to the
+# MATHJAX_RELPATH should be ../mathjax. The default value points to
-# mathjax.org site, so you can quickly see the result without installing
+# the MathJax Content Delivery Network so you can quickly see the result without
-# MathJax, but it is strongly recommended to install a local copy of MathJax
+# installing MathJax.
-# before deployment.
+# However, it is strongly recommended to install a local
+# copy of MathJax from http://www.mathjax.org before deployment.
 
 MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
 
@@ -1521,22 +1559,18 @@ SKIP_FUNCTION_MACROS   = YES
 # Configuration::additions related to external references
 #---------------------------------------------------------------------------
 
-# The TAGFILES option can be used to specify one or more tagfiles.
+# The TAGFILES option can be used to specify one or more tagfiles. For each
-# Optionally an initial location of the external documentation
+# tag file the location of the external documentation should be added. The
-# can be added for each tagfile. The format of a tag file without
+# format of a tag file without this location is as follows:
-# this location is as follows:
 #
 # TAGFILES = file1 file2 ...
 # Adding location for the tag files is done as follows:
 #
 # TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths or
+# where "loc1" and "loc2" can be relative or absolute paths
-# URLs. If a location is present for each tag, the installdox tool
+# or URLs. Note that each tag file must have a unique name (where the name does
-# does not have to be run to correct the links.
+# NOT include the path). If a tag file is not located in the directory in which
-# Note that each tag file must have a unique name
+# doxygen is run, you must also specify the path to the tagfile here.
-# (where the name does NOT include the path)
-# If a tag file is not located in the directory in which doxygen
-# is run, you must also specify the path to the tagfile here.
 
 TAGFILES               =
 
@@ -1627,7 +1661,7 @@ DOT_FONTPATH           =
 # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
 # will generate a graph for each documented class showing the direct and
 # indirect inheritance relations. Setting this tag to YES will force the
-# the CLASS_DIAGRAMS tag to NO.
+# CLASS_DIAGRAMS tag to NO.
 
 CLASS_GRAPH            = YES
 
@@ -1649,6 +1683,15 @@ GROUP_GRAPHS           = YES
 
 UML_LOOK               = NO
 
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside
+# the class node. If there are many fields or methods and many nodes the
+# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
+# threshold limits the number of items for each type to make the size more
+# managable. Set this to 0 for no limit. Note that the threshold may be
+# exceeded by 50% before the limit is enforced.
+
+UML_LIMIT_NUM_FIELDS   = 10
+
 # If set to YES, the inheritance and collaboration graphs will show the
 # relations between templates and their instances.