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/C05_TutorialAdvancedInitialization.dox

@@ -1,7 +1,6 @@
 namespace Eigen {
 
-/** \page TutorialAdvancedInitialization Tutorial page 5 - Advanced initialization
-    \ingroup Tutorial
+/** \eigenManualPage TutorialAdvancedInitialization Advanced initialization
 
 \li \b Previous: \ref TutorialBlockOperations
 \li \b Next: \ref TutorialLinearAlgebra
@@ -10,7 +9,7 @@ This page discusses several advanced methods for initializing matrices. It gives
 comma-initializer, which was introduced before. It also explains how to get special matrices such as the
 identity matrix and the zero matrix.
 
-\tableofcontents
+\eigenAutoToc
 
 \section TutorialAdvancedInitializationCommaInitializer The comma initializer