diff --git a/etc/doc/HumanoidRobotAPI.Doxyfile.in b/etc/doc/HumanoidRobotAPI.Doxyfile.in
index b94498908ad50dc143238c1ec706948840d895bd..6f90b1e3a6453a9b83de402d1690c658a40bf00e 100644
--- a/etc/doc/HumanoidRobotAPI.Doxyfile.in
+++ b/etc/doc/HumanoidRobotAPI.Doxyfile.in
@@ -514,11 +514,9 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = "@PROJECT_SOURCE_DIR@/applications" \
-                                "@PROJECT_SOURCE_DIR@/core" \
-                                "@PROJECT_SOURCE_DIR@/motioncontrol" \
-						 "@PROJECT_DOC_DIR@/doxygen" \
-					     "@PROJECT_BUILD_DIR@/propertydocs.dox"
+INPUT                  = "@PROJECT_SOURCE_DIR@/source" \
+                         "@PROJECT_DOCUMENTATION_PAGES_DIR@" \
+                         "@PROJECT_BUILD_DIR@/propertydocs.dox"
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -586,7 +584,7 @@ EXCLUDE_SYMBOLS        =
 # directories that contain example code fragments that are included (see
 # the \include command).
 
-EXAMPLE_PATH           = doxygen/snippets
+EXAMPLE_PATH           = @PROJECT_DOCUMENTATION_SNIPPET_DIR_REL@
 
 # 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
@@ -606,7 +604,7 @@ EXAMPLE_RECURSIVE      = NO
 # directories that contain image that are included in the documentation (see
 # the \image command).
 
-IMAGE_PATH             = doxygen/images
+IMAGE_PATH             = @PROJECT_DOCUMENTATION_IMAGE_DIR_REL@
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -724,7 +722,7 @@ GENERATE_HTML          = YES
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `html' will be used as the default path.
 
-HTML_OUTPUT            = html
+HTML_OUTPUT            = @PROJECT_DOCUMENTATION_HTML_OUTPUT_DIR_REL@
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for
 # each generated HTML page (for example: .htm,.php,.asp). If it is left blank
@@ -736,13 +734,13 @@ HTML_FILE_EXTENSION    = .html
 # each generated HTML page. If it is left blank doxygen will generate a
 # standard header.
 
-HTML_HEADER            = doxygen/Header.html
+HTML_HEADER            = @PROJECT_DOCUMENTATION_LAYOUT_DIR_REL@/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            = doxygen/Footer.html
+HTML_FOOTER            = @PROJECT_DOCUMENTATION_LAYOUT_DIR_REL@/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
@@ -751,7 +749,7 @@ HTML_FOOTER            = doxygen/Footer.html
 # the style sheet file to the HTML output directory, so don't put your own
 # stylesheet in the HTML output directory as well, or it will be erased!
 
-HTML_STYLESHEET        = Doxygen.css
+HTML_STYLESHEET        = @PROJECT_DOCUMENTATION_LAYOUT_DIR_REL@/Doxygen.css
 
 # 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