Remove options that are stored in the common template

The Doxylocal file now only contains things that are specific to this
project (although most projects still does it like this)

Documentation/Doxylocal

@@ -13,49 +13,14 @@ INPUT                  = @PROJECT_SOURCE_DIR@/@src_DIR@/ \
 
 EXCLUDE                =  @PROJECT_SOURCE_DIR@/@src_DIR@/core/utility/parameters/tinyxml
 
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
-
-STRIP_FROM_PATH        = @PROJECT_SOURCE_DIR@
-
 # 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 command).
 
 EXAMPLE_PATH           = @PROJECT_SOURCE_DIR@/tutorials/
 
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
-
-OUTPUT_DIRECTORY       = @PROJECT_BINARY_DIR@/@doxy_dir@
-
 # 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             = @PROJECT_SOURCE_DIR@/@doxy_dir@/Figure
-
-# 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. The 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@/@doxy_dir@/DoxygenLayout.xml
-
-# 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 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.
-
-HTML_EXTRA_STYLESHEET  = style.css