Update Doxyfile for Doxygen 1.8.8

Simply ran: doxygen -u Doxyfile.in

include/Doxyfile.in

@@ -1,4 +1,4 @@
-# Doxyfile 1.8.5
+# Doxyfile 1.8.8
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -38,7 +38,7 @@ PROJECT_NAME           = "PMDA++"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 0.4.0
+PROJECT_NUMBER         = 0.4.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -70,15 +70,25 @@ OUTPUT_DIRECTORY       =
 
 CREATE_SUBDIRS         = NO
 
+# 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
+# U+3044.
+# The default value is: NO.
+
+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, Brazilian, Catalan, Chinese, Chinese-
-# Traditional, Croatian, Czech, Danish, Dutch, English, Esperanto, Farsi,
-# Finnish, French, German, Greek, Hungarian, Italian, Japanese, Japanese-en,
-# Korean, Korean-en, Latvian, Norwegian, Macedonian, Persian, Polish,
-# Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish,
-# Turkish, Ukrainian and Vietnamese.
+# 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.
 # The default value is: English.
 
 OUTPUT_LANGUAGE        = English
@@ -259,9 +269,12 @@ OPTIMIZE_OUTPUT_VHDL   = NO
 # extension. Doxygen has a built-in mapping, but you can override or extend it
 # using this tag. The format is ext=language, where ext is a file extension, and
 # language is one of the parsers supported by doxygen: IDL, Java, Javascript,
-# C#, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL. For instance to make
-# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
-# (default is Fortran), use: inc=Fortran f=C.
+# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran:
+# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran:
+# Fortran. In the later case the parser tries to guess whether the code is fixed
+# or free formatted code, this is the default for Fortran type files), VHDL. For
+# instance to make doxygen treat .inc files as Fortran files (default is PHP),
+# and .f files as C (default is Fortran), use: inc=Fortran f=C.
 #
 # Note For files without extension you can use no_extension as a placeholder.
 #
@@ -500,6 +513,13 @@ HIDE_SCOPE_NAMES       = NO
 
 SHOW_INCLUDE_FILES     = YES
 
+# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
+# grouped member an include statement to the documentation, telling the reader
+# which file to include in order to use the member.
+# The default value is: NO.
+
+SHOW_GROUPED_MEMB_INC  = NO
+
 # If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
 # files with double quotes in the documentation rather than with sharp brackets.
 # The default value is: NO.
@@ -521,7 +541,8 @@ SORT_MEMBER_DOCS       = YES
 
 # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
 # descriptions of file, namespace and class members alphabetically by member
-# name. If set to NO the members will appear in declaration order.
+# name. If set to NO the members will appear in declaration order. Note that
+# this will also influence the order of the classes in the class list.
 # The default value is: NO.
 
 SORT_BRIEF_DOCS        = NO
@@ -659,8 +680,7 @@ LAYOUT_FILE            =
 # 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. To use this feature you need bibtex and perl available in the
-# search path. Do not use file names with spaces, bibtex cannot handle them. See
-# also \cite for info how to create references.
+# search path. See also \cite for info how to create references.
 
 CITE_BIB_FILES         =
 
@@ -797,7 +817,7 @@ EXCLUDE_PATTERNS       =
 
 EXCLUDE_SYMBOLS        = PCP_CPP_BEGIN_NAMESPACE \
                          PCP_CPP_END_NAMESPACE \
-                         PCP_CPP_EXPORT \
+                         PCP_CPP_EXPORT
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or directories
 # that contain example code fragments that are included (see the \include
@@ -959,6 +979,25 @@ USE_HTAGS              = NO
 
 VERBATIM_HEADERS       = YES
 
+# If the CLANG_ASSISTED_PARSING tag is set to YES, then doxygen will use the
+# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
+# cost of reduced performance. This can be particularly helpful with template
+# rich C++ code for which doxygen's built-in parser lacks the necessary type
+# information.
+# Note: The availability of this option depends on whether or not doxygen was
+# compiled with the --with-libclang option.
+# The default value is: NO.
+
+CLANG_ASSISTED_PARSING = NO
+
+# 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
+# the include paths will already be set by doxygen for the files and directories
+# specified with INPUT and INCLUDE_PATH.
+# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
+
+CLANG_OPTIONS          =
+
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
@@ -1051,13 +1090,15 @@ HTML_FOOTER            =
 
 HTML_STYLESHEET        =
 
-# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user-
-# defined cascading style sheet that is included after the standard style sheets
+# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
+# cascading style sheets that are included after the standard style sheets
 # created by doxygen. Using this option one can overrule certain style aspects.
 # This is preferred over using HTML_STYLESHEET since it does not replace the
 # standard style sheet and is therefor more robust against future updates.
-# Doxygen will copy the style sheet file to the output directory. For an example
-# see the documentation.
+# Doxygen will copy the style sheet files to the output directory.
+# Note: The order of the extra stylesheet files is of importance (e.g. the last
+# stylesheet in the list overrules the setting of the previous ones in the
+# list). For an example see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
 HTML_EXTRA_STYLESHEET  =
@@ -1222,7 +1263,8 @@ GENERATE_CHI           = NO
 CHM_INDEX_ENCODING     =
 
 # The BINARY_TOC flag controls whether a binary table of contents is generated (
-# YES) or a normal table of contents ( NO) in the .chm file.
+# YES) or a normal table of contents ( NO) in the .chm file. Furthermore it
+# enables the Previous and Next buttons.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
@@ -1462,11 +1504,11 @@ SEARCHENGINE           = YES
 
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be
 # implemented using a web server instead of a web client using Javascript. There
-# are two flavours of web server based searching depending on the
-# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for
-# searching and an index file used by the script. When EXTERNAL_SEARCH is
-# enabled the indexing and searching needs to be provided by external tools. See
-# the section "External Indexing and Searching" for details.
+# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
+# setting. When disabled, doxygen will generate a PHP script for searching and
+# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
+# and searching needs to be provided by external tools. See the section
+# "External Indexing and Searching" for details.
 # The default value is: NO.
 # This tag requires that the tag SEARCHENGINE is set to YES.
 
@@ -1594,17 +1636,19 @@ EXTRA_PACKAGES         =
 #
 # Note: Only use a user-defined header if you know what you are doing! The
 # following commands have a special meaning inside the header: $title,
-# $datetime, $date, $doxygenversion, $projectname, $projectnumber. Doxygen will
-# replace them by respectively the title of the page, the current date and time,
-# only the current date, the version number of doxygen, the project name (see
-# PROJECT_NAME), or the project number (see PROJECT_NUMBER).
+# $datetime, $date, $doxygenversion, $projectname, $projectnumber,
+# $projectbrief, $projectlogo. Doxygen will replace $title with the empy string,
+# for the replacement values of the other commands the user is refered to
+# HTML_HEADER.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
 LATEX_HEADER           =
 
 # The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the
 # generated LaTeX document. The footer should contain everything after the last
-# chapter. If it is left blank doxygen will generate a standard footer.
+# chapter. If it is left blank doxygen will generate a standard footer. See
+# LATEX_HEADER for more information on how to generate a default footer and what
+# special commands can be used inside the footer.
 #
 # Note: Only use a user-defined footer if you know what you are doing!
 # This tag requires that the tag GENERATE_LATEX is set to YES.
@@ -1628,7 +1672,7 @@ LATEX_EXTRA_FILES      =
 
 PDF_HYPERLINKS         = YES
 
-# If the LATEX_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
 # the PDF file directly from the LaTeX files. Set this option to YES to get a
 # higher quality PDF documentation.
 # The default value is: YES.
@@ -1754,6 +1798,13 @@ MAN_OUTPUT             = man
 
 MAN_EXTENSION          = .3
 
+# The MAN_SUBDIR tag determines the name of the directory created within
+# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
+# MAN_EXTENSION with the initial . removed.
+# This tag requires that the tag GENERATE_MAN is set to YES.
+
+MAN_SUBDIR             =
+
 # If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
 # will generate one additional man file for each entity documented in the real
 # man page(s). These additional files only source the real man page, but without
@@ -1781,18 +1832,6 @@ GENERATE_XML           = NO
 
 XML_OUTPUT             = xml
 
-# The XML_SCHEMA tag can be used to specify a XML schema, which can be used by a
-# validating XML parser to check the syntax of the XML files.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_SCHEMA             =
-
-# The XML_DTD tag can be used to specify a XML DTD, which can be used by a
-# validating XML parser to check the syntax of the XML files.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_DTD                =
-
 # If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program
 # listings (including syntax highlighting and cross-referencing information) to
 # the XML output. Note that enabling this will significantly increase the size
@@ -1820,6 +1859,15 @@ GENERATE_DOCBOOK       = NO
 
 DOCBOOK_OUTPUT         = docbook
 
+# If the DOCBOOK_PROGRAMLISTING tag is set to YES doxygen will include the
+# program listings (including syntax highlighting and cross-referencing
+# information) to the DOCBOOK output. Note that enabling this will significantly
+# increase the size of the DOCBOOK output.
+# The default value is: NO.
+# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
+
+DOCBOOK_PROGRAMLISTING = NO
+
 #---------------------------------------------------------------------------
 # Configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
@@ -1939,9 +1987,9 @@ PREDEFINED             =
 EXPAND_AS_DEFINED      =
 
 # If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
-# remove all refrences to function-like macros that are alone on a line, have an
-# all uppercase name, and do not end with a semicolon. Such function macros are
-# typically used for boiler-plate code, and will confuse the parser if not
+# remove all references to function-like macros that are alone on a line, have
+# an all uppercase name, and do not end with a semicolon. Such function macros
+# are typically used for boiler-plate code, and will confuse the parser if not
 # removed.
 # The default value is: YES.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
@@ -1961,7 +2009,7 @@ SKIP_FUNCTION_MACROS   = YES
 # where loc1 and loc2 can be relative or absolute paths or URLs. See the
 # section "Linking to external documentation" for more information about the use
 # of tag files.
-# Note: Each tag file must have an unique name (where the name does NOT include
+# Note: Each tag file must have a unique name (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.
 
@@ -2021,6 +2069,13 @@ CLASS_DIAGRAMS         = YES
 
 MSCGEN_PATH            =
 
+# You can include diagrams made with dia in doxygen documentation. Doxygen will
+# then run dia to produce the diagram and insert it in the documentation. The
+# DIA_PATH tag allows you to specify the directory where the dia binary resides.
+# If left empty dia is assumed to be found in the default search path.
+
+DIA_PATH               =
+
 # If set to YES, the inheritance and collaboration graphs will hide inheritance
 # and usage relations if the target is undocumented or is not a class.
 # The default value is: YES.
@@ -2032,7 +2087,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
 # Bell Labs. The other options in this section have no effect if this option is
 # set to NO
-# The default value is: NO.
+# The default value is: YES.
 
 HAVE_DOT               = ${DOXYGEN_DOT_FOUND}
 
@@ -2046,7 +2101,7 @@ HAVE_DOT               = ${DOXYGEN_DOT_FOUND}
 
 DOT_NUM_THREADS        = 0
 
-# When you want a differently looking font n the dot files that doxygen
+# 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
@@ -2184,7 +2239,9 @@ DIRECTORY_GRAPH        = YES
 # Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
 # to make the SVG files visible in IE 9+ (other browsers do not have this
 # requirement).
-# Possible values are: png, jpg, gif and svg.
+# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd,
+# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo,
+# gif:cairo:gd, gif:gd, gif:gd:gd and svg.
 # The default value is: png.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
@@ -2221,6 +2278,21 @@ DOTFILE_DIRS           =
 
 MSCFILE_DIRS           =
 
+# The DIAFILE_DIRS tag can be used to specify one or more directories that
+# contain dia files that are included in the documentation (see the \diafile
+# command).
+
+DIAFILE_DIRS           =
+
+# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
+# path where java can find the plantuml.jar file. If left blank, it is assumed
+# PlantUML is not used or called during a preprocessing step. Doxygen will
+# generate a warning when it encounters a \startuml command in this case and
+# will not generate output for the diagram.
+# This tag requires that the tag HAVE_DOT is set to YES.
+
+PLANTUML_JAR_PATH      =
+
 # The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
 # that will be shown in the graph. If the number of nodes in a graph becomes
 # larger than this value, doxygen will truncate the graph, which is visualized