Big changes in Eigen documentation:

- Organize the documentation into "chapters".
  - Each chapter include many documentation pages, reference pages organized as modules, and a quick reference page.
  - The "Chapters" tree is created using the defgroup/ingroup mechanism, even for the documentation pages (i.e., .dox files for which I added an \eigenManualPage macro that we can switch between \page or \defgroup ).
  - Add a "General topics" entry for all pages that do not fit well in the previous "chapters".
  - The highlevel struture is managed by a new eigendoxy_layout.xml file.
- remove the "index" and quite useless pages (namespace list, class hierarchy, member list, file list, etc.)
- add the javascript search-engine.
- add the "treeview" panel.
- remove \tableofcontents (replace them by a custom \eigenAutoToc macro to be able to easily re-enable if needed).
- add javascript to automatically generate a TOC from the h1/h2 tags of the current page, and put the TOC in the left side panel.
- overload various javascript function generated by doxygen to:
  - remove the root of the treeview
  - remove links to section/subsection from the treeview
  - automatically expand the "Chapters" section
  - automatically expand the current section
  - adjust the height of the treeview to take into account the TOC
- always use the default .css file, eigendoxy.css now only includes our modifications
- use Doxyfile to specify our logo
- remove cross references to unsupported modules (temporarily)

doc/Doxyfile.in

@@ -47,7 +47,7 @@ PROJECT_BRIEF          =
 # exceed 55 pixels and the maximum width should not exceed 200 pixels.
 # Doxygen will copy the logo to the output directory.
 
-PROJECT_LOGO           =
+PROJECT_LOGO           = "${Eigen_SOURCE_DIR}/doc/Eigen_Silly_Professor_64x64.png"
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
@@ -223,6 +223,9 @@ ALIASES                = "only_for_vectors=This is only for vectors (either row-
                          "note_about_checking_solutions=This method just tries to find as good a solution as possible. If you want to check whether a solution exists or if it is accurate, just call this function to get a result and then compute the error of this result, or use MatrixBase::isApprox() directly, for instance like this: \code bool a_solution_exists = (A*result).isApprox(b, precision); \endcode This method avoids dividing by zero, so that the non-existence of a solution doesn't by itself mean that you'll get \c inf or \c nan values." \
                          "note_try_to_help_rvo=This function returns the result by value. In order to make that efficient, it is implemented as just a return statement using a special constructor, hopefully allowing the compiler to perform a RVO (return value optimization)."
 
+ALIASES += "eigenAutoToc=  "
+ALIASES += "eigenManualPage=\defgroup"
+
 # 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
@@ -474,7 +477,7 @@ HIDE_SCOPE_NAMES       = YES
 # will put a list of the files that are included by a file in the documentation
 # of that file.
 
-SHOW_INCLUDE_FILES     = YES
+SHOW_INCLUDE_FILES     = NO
 
 # If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
 # will list include files with double quotes in the documentation
@@ -592,7 +595,7 @@ SHOW_FILES             = YES
 # 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
+SHOW_NAMESPACES        = NO
 
 # The FILE_VERSION_FILTER tag can be used to specify a program or script that
 # doxygen should invoke to get the current version for each file (typically from
@@ -611,7 +614,7 @@ FILE_VERSION_FILTER    =
 # 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            = 
+LAYOUT_FILE            = "${Eigen_BINARY_DIR}/doc/eigendoxy_layout.xml"
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files
 # containing the references data. This must be a list of .bib files. The
@@ -954,7 +957,7 @@ HTML_FOOTER            = "${Eigen_BINARY_DIR}/doc/eigendoxy_footer.html"
 # 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        = "${Eigen_SOURCE_DIR}/doc/eigendoxy.css"
+HTML_STYLESHEET        = 
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
@@ -963,7 +966,7 @@ HTML_STYLESHEET        = "${Eigen_SOURCE_DIR}/doc/eigendoxy.css"
 # files. In the HTML_STYLESHEET file, use the file name only. Also note that
 # the files will be copied as-is; there are no commands or markers available.
 
-HTML_EXTRA_FILES       =
+HTML_EXTRA_FILES       = "${Eigen_SOURCE_DIR}/doc/eigendoxy.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
@@ -972,6 +975,7 @@ HTML_EXTRA_FILES       =
 # 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
 
@@ -1170,7 +1174,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # navigation tree you can set this option to NO if you already set
 # GENERATE_TREEVIEW to YES.
 
-DISABLE_INDEX          = NO
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
@@ -1182,7 +1186,7 @@ DISABLE_INDEX          = NO
 # 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      = NO
+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
@@ -1252,7 +1256,7 @@ MATHJAX_EXTENSIONS     =
 # typically be disabled. For large projects the javascript based search engine
 # can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
 
-SEARCHENGINE           = NO
+SEARCHENGINE           = YES
 
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be
 # implemented using a PHP enabled web server instead of at the web client
@@ -1614,7 +1618,8 @@ SKIP_FUNCTION_MACROS   = YES
 # 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               = "${Eigen_BINARY_DIR}/doc/eigen-unsupported.doxytags =unsupported"
+TAGFILES               = 
+# "${Eigen_BINARY_DIR}/doc/eigen-unsupported.doxytags =unsupported"
 
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create
 # a tag file that is based on the input files it reads.