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)

Eigen/Core

@@ -242,10 +242,6 @@ using std::ptrdiff_t;
   * \endcode
   */
 
-/** \defgroup Support_modules Support modules [category]
-  * Category of modules which add support for external libraries.
-  */
-
 #include "src/Core/util/Constants.h"
 #include "src/Core/util/ForwardDeclarations.h"
 #include "src/Core/util/Meta.h"

Eigen/IterativeLinearSolvers

@@ -6,7 +6,7 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-/** \ingroup Sparse_modules
+/** 
   * \defgroup IterativeLinearSolvers_Module IterativeLinearSolvers module
   *
   * This module currently provides iterative methods to solve problems of the form \c A \c x = \c b, where \c A is a squared matrix, usually very large and sparse.

Eigen/OrderingMethods

@@ -5,7 +5,7 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-/** \ingroup Sparse_modules
+/** 
   * \defgroup OrderingMethods_Module OrderingMethods module
   *
   * This module is currently for internal use only.

Eigen/Sparse

@@ -1,7 +1,7 @@
 #ifndef EIGEN_SPARSE_MODULE_H
 #define EIGEN_SPARSE_MODULE_H
 
-/** \defgroup Sparse_modules Sparse modules
+/** defgroup Sparse_modules Sparse modules
   *
   * Meta-module including all related modules:
   * - SparseCore

Eigen/SparseCholesky

@@ -5,7 +5,7 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-/** \ingroup Sparse_modules
+/** 
   * \defgroup SparseCholesky_Module SparseCholesky module
   *
   * This module currently provides two variants of the direct sparse Cholesky decomposition for selfadjoint (hermitian) matrices.

Eigen/SparseCore

@@ -11,7 +11,7 @@
 #include <cstring>
 #include <algorithm>
 
-/** \ingroup Sparse_modules
+/** 
   * \defgroup SparseCore_Module SparseCore module
   *
   * This module provides a sparse matrix representation, and basic associatd matrix manipulations

Eigen/SparseLU

@@ -4,7 +4,7 @@
 #include "SparseCore"
 
 
-/** \ingroup Sparse_modules
+/** 
   * \defgroup SparseLU_Module SparseLU module
   *
   */