diff --git a/doc/Doxyfile.extra.in b/doc/Doxyfile.extra.in
index a67a7c4b0db9849793c1e44d2dbea72ff9a6bef1..fd0c463893d235ef7ffd1fbd638a48ea6a8f2808 100644
--- a/doc/Doxyfile.extra.in
+++ b/doc/Doxyfile.extra.in
@@ -1,7 +1,611 @@
-INPUT = @CMAKE_SOURCE_DIR@/src \
- @CMAKE_SOURCE_DIR@/doc/additionalDoc
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB = NO
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+# (but less readable) file names. This can be useful is your file systems
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like regular Qt-style comments
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF = NO
+
+# 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
+
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
+# unions are shown inside the group in which they are included (e.g. using
+# @ingroup) instead of on a separate page (for HTML and Man pages) or
+# section (for LaTeX and RTF).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penalty.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# 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.
+
+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
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# 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 HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+#HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+#HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = YES
+
+# 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.
+
+HIDE_SCOPE_NAMES = YES
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS = DEV
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
+# will sort the (brief and detailed) documentation of class members so that
+# constructors and destructors are listed first. If set to NO (the default)
+# the constructors will appear in the respective orders defined by
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = YES
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# do proper type resolution of all parameters of a function it will reject a
+# match between the prototype and the implementation of a member function even
+# if there is only one candidate or it is obvious which candidate to choose
+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
+# will still accept a match between prototype and implementation in such cases.
+
+STRICT_PROTO_MATCHING = NO
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or define consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and defines in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page.
+# This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# If the sources in your project are distributed over multiple directories
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES = YES
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option.
+# You can optionally specify a file name after the option, if omitted
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE = @PROJECT_SOURCE_DIR@/doc/layout.xml
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR = YES
+
+# The WARN_NO_PARAMDOC option can be enabled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT = "$file:$line: $text"
+
+# 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 stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT = @CMAKE_SOURCE_DIR@/doc/additionalDoc \
+ @CMAKE_SOURCE_DIR@/doc \
+ @CMAKE_SOURCE_DIR@/src
+
+# 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.
+# If left blank NO is used.
+
+RECURSIVE = YES
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+
+FILE_PATTERNS = *.cc *.cpp *.h *.hpp *.hxx *.hh *.dox
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. 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 += CMake* \
+ *.txt \
+ *.sh \
+ *.orig \
+ *.diff \
+ diff \
+ *~ \
+ *. \
+ *.sln \
+ *.sdf \
+ *.tmp \
+ *.vcxproj \
+ *.filters \
+ *.user \
+ *.suo
+
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS = internal::*
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
IMAGE_PATH = @CMAKE_SOURCE_DIR@/doc/pictures
-FILE_PATTERNS = *.cc *.cpp *.h *.hpp *.hxx *.hh
-TAGFILES = \
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = YES
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 4
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# 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 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
+# changing the value of configuration settings such as GENERATE_TREEVIEW!
+
+HTML_HEADER = @PROJECT_SOURCE_DIR@/doc/header.html
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER = @PROJECT_SOURCE_DIR@/doc/footer.html
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If the tag is left blank doxygen
+# will generate a default style sheet. Note that doxygen will try to copy
+# the style sheet file to the HTML output directory, so don't put your own
+# style sheet in the HTML output directory as well, or it will be erased!
+
+#HTML_STYLESHEET = @PROJECT_SOURCE_DIR@/doc/package.css
+
+# 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 colorwheel,
+# see http://en.wikipedia.org/wiki/Hue for more information.
+# For instance the value 0 represents red, 60 is yellow, 120 is green,
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
+# The allowed range is 0 to 359.
+# The default is 220.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
+# the colors in the HTML output. For a value of 0 the output will use
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
+# the luminance component of the colors in the HTML output. Values below
+# 100 gradually make the output lighter, whereas values above 100 make
+# the output darker. The value divided by 100 is the actual gamma applied,
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded. For this to work a browser that supports
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = org.doxygen.@PACKAGE_NAME@
+
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+
+DOCSET_PUBLISHER_ID = fr.laas.gepetto
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME = Gepetto
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE = org.doxygen.@PACKAGE_NAME@
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID = org.doxygen.@PACKAGE_NAME@
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it.
+
+DISABLE_INDEX = YES
+
+# 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
+# containing a tree-like index structure (just like the one that
+# 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
+
+# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
+# and Class Hierarchy pages using a tree view instead of an ordered list.
+
+USE_INLINE_TREES = YES
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 12
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = YES
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES += leftidx
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED += WITH_HPP_FCL
+
+# 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.
+
+INCLUDE_PATH += @PROJECT_SOURCE_DIR@/src \
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles.
+# Optionally an initial location of the external documentation
+# can be added for each tagfile. The format of a tag file without
+# 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
+# URLs. If a location is present for each tag, the installdox tool
+# does not have to be run to correct the links.
+# Note that 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.
+
+TAGFILES =
+
+
diff --git a/doc/footer.html b/doc/footer.html
index 535d304e7f00b9b77241c4bf6e63e883164c570c..878244a1996d0216f22ab076f4a87e7182615630 100644
--- a/doc/footer.html
+++ b/doc/footer.html
@@ -1,11 +1,36 @@
- <br><br>
- <hr>
- <center>
- <img src="./pictures/footer.jpg" Height=100>
- <br>soth library documentation</br>
- </center>
- <hr>
- </center>
- </body>
- </head>
+<!-- start footer part -->
+<!--BEGIN GENERATE_TREEVIEW-->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ $navpath
+ <li class="footer">$generatedby
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="$relpath$doxygen.png" alt="doxygen"/></a> $doxygenversion </li>
+ </ul>
+</div>
+<!--END GENERATE_TREEVIEW-->
+<!--BEGIN !GENERATE_TREEVIEW-->
+<hr class="footer"/><address class="footer"><small>
+$generatedby  <a href="http://www.doxygen.org/index.html">
+<img class="footer" src="$relpath$doxygen.png" alt="doxygen"/>
+</a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+
+<!-- Piwik -->
+<script type="text/javascript">
+var pkBaseURL = (("https:" == document.location.protocol) ? "https://stats.sylphide-consulting.com/piwik/" : "http://stats.sylphide-consulting.com/piwik/");
+document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E"));
+</script><script type="text/javascript">
+try {
+var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", 20);
+piwikTracker.trackPageView();
+piwikTracker.enableLinkTracking();
+} catch( err ) {}
+</script><noscript><p><img src="http://stats.sylphide-consulting.com/piwik/piwik.php?idsite=20" style="border:0" alt="" /></p></noscript>
+<!-- End Piwik Tracking Code -->
+
+</body>
+</html>
+
diff --git a/doc/header.html b/doc/header.html
index ca3e578a0a37b115093297273260a2729989cf19..70e64b796940f43c66ae7862eb49c72aa9a586a9 100644
--- a/doc/header.html
+++ b/doc/header.html
@@ -1,7 +1,60 @@
-<HTML>
- <HEAD>
- <TITLE>soth library documentation</TITLE>
- <LINK HREF="package.css" REL="stylesheet" TYPE="text/css">
- </HEAD>
- <BODY>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen $doxygenversion"/>
+<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+<link href="$relpath$tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="$relpath$jquery.js"></script>
+<script type="text/javascript" src="$relpath$dynsections.js"></script>
+$treeview
+$search
+$mathjax
+<link href="$relpath$$stylesheet" rel="stylesheet" type="text/css" />
+<link href="$relpath$eigendoxy.css" rel="stylesheet" type="text/css">
+<!-- $extrastylesheet -->
+<script type="text/javascript" src="$relpath$eigen_navtree_hacks.js"></script>
+<!-- <script type="text/javascript"> -->
+<!-- </script> -->
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<!-- <a name="top"></a> -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <!--BEGIN PROJECT_LOGO-->
+ <td id="projectlogo"><img alt="Logo" src="$relpath$$projectlogo"/></td>
+ <!--END PROJECT_LOGO-->
+ <!--BEGIN PROJECT_NAME-->
+ <td style="padding-left: 0.5em;">
+ <div id="projectname"><a href="https://github.com/stack-of-tasks/pinocchio">$projectname</a>
+ <!--BEGIN PROJECT_NUMBER--> <span id="projectnumber">$projectnumber</span><!--END PROJECT_NUMBER-->
+ </div>
+ <!--BEGIN PROJECT_BRIEF--><div id="projectbrief">Dynamic computations using Spatial Algebra</div><!--END PROJECT_BRIEF-->
+ </td>
+ <!--END PROJECT_NAME-->
+ <!--BEGIN !PROJECT_NAME-->
+ <!--BEGIN PROJECT_BRIEF-->
+ <td style="padding-left: 0.5em;">
+ <div id="projectbrief">$projectbrief</div>
+ </td>
+ <!--END PROJECT_BRIEF-->
+ <!--END !PROJECT_NAME-->
+ <!--BEGIN DISABLE_INDEX-->
+ <!--BEGIN SEARCHENGINE-->
+ <td>$searchbox</td>
+ <!--END SEARCHENGINE-->
+ <!--END DISABLE_INDEX-->
+ </tr>
+ </tbody>
+</table>
+</div>
+<!--END TITLEAREA-->
+<!-- end header part -->
diff --git a/doc/layout.xml b/doc/layout.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3fb457ffc6c2c8163dfc95919a69e0c67347e93e
--- /dev/null
+++ b/doc/layout.xml
@@ -0,0 +1,190 @@
+<doxygenlayout version="1.0">
+ <!-- Navigation index tabs for HTML output -->
+ <navindex>
+ <tab type="mainpage" visible="yes" title="hello"/>
+ <tab type="pages" visible="yes" title="Getting Started" intro=""/>
+ <tab type="modules" visible="yes" title="" intro=""/>
+<!-- <tab type="namespaces" visible="yes" title="">
+ <tab type="namespacelist" visible="yes" title="" intro=""/>
+ <tab type="namespacemembers" visible="yes" title="" intro=""/>
+ </tab>
+ -->
+ <tab type="classes" visible="yes" title="">
+ <tab type="classlist" visible="yes" title="" intro=""/>
+ <tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/>
+ <tab type="hierarchy" visible="yes" title="" intro=""/>
+ <tab type="classmembers" visible="yes" title="" intro=""/>
+ </tab>
+<!-- <tab type="files" visible="yes" title="">
+ <tab type="filelist" visible="yes" title="" intro=""/>
+ <tab type="globals" visible="yes" title="" intro=""/>
+ </tab>
+ -->
+ <tab type="dirs" visible="yes" title="" intro=""/>
+ <tab type="examples" visible="yes" title="" intro=""/>
+ </navindex>
+
+ <!-- Layout definition for a class page -->
+ <class>
+ <briefdescription visible="yes"/>
+ <includes visible="$SHOW_INCLUDE_FILES"/>
+ <inheritancegraph visible="$CLASS_GRAPH"/>
+ <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+ <allmemberslink visible="yes"/>
+ <memberdecl>
+ <nestedclasses visible="yes" title=""/>
+ <publictypes title=""/>
+ <publicslots title=""/>
+ <signals title=""/>
+ <publicmethods title=""/>
+ <publicstaticmethods title=""/>
+ <publicattributes title=""/>
+ <publicstaticattributes title=""/>
+ <protectedtypes title=""/>
+ <protectedslots title=""/>
+ <protectedmethods title=""/>
+ <protectedstaticmethods title=""/>
+ <protectedattributes title=""/>
+ <protectedstaticattributes title=""/>
+ <packagetypes title=""/>
+ <packagemethods title=""/>
+ <packagestaticmethods title=""/>
+ <packageattributes title=""/>
+ <packagestaticattributes title=""/>
+ <properties title=""/>
+ <events title=""/>
+ <privatetypes title=""/>
+ <privateslots title=""/>
+ <privatemethods title=""/>
+ <privatestaticmethods title=""/>
+ <privateattributes title=""/>
+ <privatestaticattributes title=""/>
+ <friends title=""/>
+ <related title="" subtitle=""/>
+ <membergroups visible="yes"/>
+ </memberdecl>
+ <detaileddescription title=""/>
+ <memberdef>
+ <inlineclasses title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <constructors title=""/>
+ <functions title=""/>
+ <related title=""/>
+ <variables title=""/>
+ <properties title=""/>
+ <events title=""/>
+ </memberdef>
+ <usedfiles visible="$SHOW_USED_FILES"/>
+ <authorsection visible="yes"/>
+ </class>
+
+ <!-- Layout definition for a namespace page -->
+ <namespace>
+ <briefdescription visible="yes"/>
+ <memberdecl>
+ <nestednamespaces visible="yes" title=""/>
+ <classes visible="yes" title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ <membergroups visible="yes"/>
+ </memberdecl>
+ <detaileddescription title=""/>
+ <memberdef>
+ <inlineclasses title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ </memberdef>
+ <authorsection visible="yes"/>
+ </namespace>
+
+ <!-- Layout definition for a file page -->
+ <file>
+ <briefdescription visible="yes"/>
+ <includes visible="$SHOW_INCLUDE_FILES"/>
+ <includegraph visible="$INCLUDE_GRAPH"/>
+ <includedbygraph visible="$INCLUDED_BY_GRAPH"/>
+ <sourcelink visible="yes"/>
+ <memberdecl>
+ <classes visible="yes" title=""/>
+ <namespaces visible="yes" title=""/>
+ <defines title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ <membergroups visible="yes"/>
+ </memberdecl>
+ <detaileddescription title=""/>
+ <memberdef>
+ <inlineclasses title=""/>
+ <defines title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ </memberdef>
+ <authorsection/>
+ </file>
+
+ <!-- Layout definition for a group page -->
+ <group>
+ <briefdescription visible="yes"/>
+ <groupgraph visible="$GROUP_GRAPHS"/>
+ <memberdecl>
+ <classes visible="yes" title=""/>
+ <namespaces visible="yes" title=""/>
+ <dirs visible="yes" title=""/>
+ <nestedgroups visible="yes" title=""/>
+ <files visible="yes" title=""/>
+ <defines title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <enumvalues title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ <signals title=""/>
+ <publicslots title=""/>
+ <protectedslots title=""/>
+ <privateslots title=""/>
+ <events title=""/>
+ <properties title=""/>
+ <friends title=""/>
+ <membergroups visible="yes"/>
+ </memberdecl>
+ <detaileddescription title=""/>
+ <memberdef>
+ <pagedocs/>
+ <inlineclasses title=""/>
+ <defines title=""/>
+ <typedefs title=""/>
+ <enums title=""/>
+ <enumvalues title=""/>
+ <functions title=""/>
+ <variables title=""/>
+ <signals title=""/>
+ <publicslots title=""/>
+ <protectedslots title=""/>
+ <privateslots title=""/>
+ <events title=""/>
+ <properties title=""/>
+ <friends title=""/>
+ </memberdef>
+ <authorsection visible="yes"/>
+ </group>
+
+ <!-- Layout definition for a directory page -->
+ <directory>
+ <briefdescription visible="yes"/>
+ <directorygraph visible="yes"/>
+ <memberdecl>
+ <dirs visible="yes"/>
+ <files visible="yes"/>
+ </memberdecl>
+ <detaileddescription title=""/>
+ </directory>
+</doxygenlayout>