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)

1 files changed, 155 insertions, 0 deletions

diff --git a/doc/Manual.dox b/doc/Manual.dox
new file mode 100644
index 000000000..69e33770e
--- /dev/null
+++ b/doc/Manual.dox
@@ -0,0 +1,155 @@
+
+// This file strutures pages and modules into a convenient hierarchical structure.
+
+namespace Eigen {
+
+/** \page UserManual_Generalities General topics
+  - \subpage Eigen2ToEigen3
+  - \subpage TopicFunctionTakingEigenTypes
+  - \subpage TopicPreprocessorDirectives
+  - \subpage TopicAssertions
+  - \subpage TopicCustomizingEigen
+  - \subpage TopicMultiThreading
+  - \subpage TopicUsingIntelMKL
+  - \subpage TopicTemplateKeyword
+  - \subpage UserManual_UnderstandingEigen
+*/
+  
+/** \page UserManual_UnderstandingEigen Understanding Eigen
+  - \subpage TopicInsideEigenExample
+  - \subpage TopicClassHierarchy
+  - \subpage TopicLazyEvaluation
+*/
+
+/** \page UnclassifiedPages Unclassified pages
+  - \subpage TopicResizing
+  - \subpage TopicVectorization
+  - \subpage TopicEigenExpressionTemplates
+  - \subpage TopicScalarTypes
+  - \subpage GettingStarted
+  - \subpage TutorialSparse_example_details
+  - \subpage TopicWritingEfficientProductExpression
+  - \subpage Experimental
+*/
+
+
+/** \defgroup Support_modules Support modules
+  * Category of modules which add support for external libraries.
+  */
+
+
+/** \defgroup DenseMatrixManipulation_chapter Dense matrix and array manipulation */
+/** \defgroup DenseMatrixManipulation_Alignement Alignment issues */
+/** \defgroup DenseMatrixManipulation_Reference Reference */
+
+/** \addtogroup TutorialMatrixClass
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup TutorialMatrixArithmetic
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup TutorialArrayClass
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup TutorialBlockOperations
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup TutorialAdvancedInitialization
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup TutorialReductionsVisitorsBroadcasting
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup TutorialMapClass
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup TopicAliasing
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup TopicStorageOrders
+    \ingroup DenseMatrixManipulation_chapter */
+    
+/** \addtogroup DenseMatrixManipulation_Alignement
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup TopicUnalignedArrayAssert
+    \ingroup DenseMatrixManipulation_Alignement */
+/** \addtogroup TopicFixedSizeVectorizable
+    \ingroup DenseMatrixManipulation_Alignement */
+/** \addtogroup TopicStructHavingEigenMembers
+    \ingroup DenseMatrixManipulation_Alignement */
+/** \addtogroup TopicStlContainers
+    \ingroup DenseMatrixManipulation_Alignement */
+/** \addtogroup TopicPassingByValue
+    \ingroup DenseMatrixManipulation_Alignement */
+/** \addtogroup TopicWrongStackAlignment
+    \ingroup DenseMatrixManipulation_Alignement */
+    
+/** \addtogroup DenseMatrixManipulation_Reference
+    \ingroup DenseMatrixManipulation_chapter */
+/** \addtogroup Core_Module
+    \ingroup DenseMatrixManipulation_Reference */  
+/** \addtogroup Jacobi_Module
+    \ingroup DenseMatrixManipulation_Reference */ 
+/** \addtogroup Householder_Module
+    \ingroup DenseMatrixManipulation_Reference */ 
+
+/** \addtogroup QuickRefPage
+    \ingroup DenseMatrixManipulation_chapter */
+
+
+/** \defgroup DenseLinearSolvers_chapter Dense linear problems and decompositions */
+/** \defgroup DenseLinearSolvers_Reference Reference */
+
+/** \addtogroup TutorialLinearAlgebra
+    \ingroup DenseLinearSolvers_chapter */
+/** \addtogroup TopicLinearAlgebraDecompositions
+    \ingroup DenseLinearSolvers_chapter */
+
+/** \addtogroup DenseLinearSolvers_Reference
+    \ingroup DenseLinearSolvers_chapter */
+/** \addtogroup Cholesky_Module
+    \ingroup DenseLinearSolvers_Reference */
+/** \addtogroup LU_Module
+    \ingroup DenseLinearSolvers_Reference */
+/** \addtogroup QR_Module
+    \ingroup DenseLinearSolvers_Reference */
+/** \addtogroup SVD_Module
+    \ingroup DenseLinearSolvers_Reference*/
+/** \addtogroup Eigenvalues_Module
+    \ingroup DenseLinearSolvers_Reference */
+
+
+
+
+/** \defgroup Sparse_chapter Sparse linear algebra */
+/** \defgroup Sparse_Reference Reference */
+
+/** \addtogroup TutorialSparse
+    \ingroup Sparse_chapter */
+/** \addtogroup TopicSparseSystems
+    \ingroup Sparse_chapter */
+
+/** \addtogroup Sparse_Reference
+    \ingroup Sparse_chapter */
+/** \addtogroup SparseCore_Module
+    \ingroup Sparse_Reference */
+/** \addtogroup OrderingMethods_Module
+    \ingroup Sparse_Reference */
+/** \addtogroup SparseCholesky_Module
+    \ingroup Sparse_Reference */
+/** \addtogroup SparseLU_Module
+    \ingroup Sparse_Reference */
+/** \addtogroup IterativeLinearSolvers_Module
+    \ingroup Sparse_Reference */
+/** \addtogroup Support_modules
+    \ingroup Sparse_Reference */    
+
+/** \addtogroup SparseQuickRefPage
+    \ingroup Sparse_chapter */
+
+
+/** \defgroup Geometry_chapter Geometry */
+/** \defgroup Geometry_Reference Reference */
+
+/** \addtogroup TutorialGeometry
+    \ingroup Geometry_chapter */
+    
+/** \addtogroup Geometry_Reference
+    \ingroup Geometry_chapter */
+/** \addtogroup Geometry_Module
+    \ingroup Geometry_Reference */
+/** \addtogroup Splines_Module
+    \ingroup Geometry_Reference */
+}