26 files changed, 11 insertions, 94 deletions
diff --git a/Eigen/src/Array/PartialRedux.h b/Eigen/src/Array/PartialRedux.h
index 27c315d6e..357654b4e 100644
--- a/Eigen/src/Array/PartialRedux.h
+++ b/Eigen/src/Array/PartialRedux.h
@@ -69,11 +69,7 @@ struct ei_traits<PartialReduxExpr<MatrixType, MemberOp, Direction> >
 
 template< typename MatrixType, typename MemberOp, int Direction>
 class PartialReduxExpr : ei_no_assignment_operator,
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   public MatrixBase<PartialReduxExpr<MatrixType, MemberOp, Direction> >
-#else
-  public MapBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/Block.h b/Eigen/src/Core/Block.h
index 4fb4794a4..11583d042 100644
--- a/Eigen/src/Core/Block.h
+++ b/Eigen/src/Core/Block.h
@@ -88,11 +88,7 @@ struct ei_traits<Block<MatrixType, BlockRows, BlockCols, _PacketAccess, _DirectA
 };
 
 template<typename MatrixType, int BlockRows, int BlockCols, int PacketAccess, int _DirectAccessStatus> class Block
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MatrixBase<Block<MatrixType, BlockRows, BlockCols, PacketAccess, _DirectAccessStatus> >
-#else
-  : public MatrixBase
-#endif
 {
   public:
 
@@ -215,11 +211,7 @@ template<typename MatrixType, int BlockRows, int BlockCols, int PacketAccess, in
 /** \internal */
 template<typename MatrixType, int BlockRows, int BlockCols, int PacketAccess>
 class Block<MatrixType,BlockRows,BlockCols,PacketAccess,HasDirectAccess>
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MapBase<Block<MatrixType, BlockRows, BlockCols,PacketAccess,HasDirectAccess> >
-#else
-  : public MapBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/CommaInitializer.h b/Eigen/src/Core/CommaInitializer.h
index c394c3d78..282510550 100644
--- a/Eigen/src/Core/CommaInitializer.h
+++ b/Eigen/src/Core/CommaInitializer.h
@@ -108,7 +108,8 @@ struct MatrixBase<Derived>::CommaInitializer
   int m_currentBlockRows; // current block height
 };
 
-/** Convenient operator to set the coefficients of a matrix.
+/** \anchor MatrixBaseCommaInitRef
+  * Convenient operator to set the coefficients of a matrix.
   *
   * The coefficients must be provided in a row major order and exactly match
   * the size of the matrix. Otherwise an assertion is raised.
diff --git a/Eigen/src/Core/CwiseBinaryOp.h b/Eigen/src/Core/CwiseBinaryOp.h
index da76ac100..ec98f4c64 100644
--- a/Eigen/src/Core/CwiseBinaryOp.h
+++ b/Eigen/src/Core/CwiseBinaryOp.h
@@ -76,11 +76,7 @@ struct ei_traits<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >
 
 template<typename BinaryOp, typename Lhs, typename Rhs>
 class CwiseBinaryOp : ei_no_assignment_operator,
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   public MatrixBase<CwiseBinaryOp<BinaryOp, Lhs, Rhs> >
-#else
-  public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/CwiseNullaryOp.h b/Eigen/src/Core/CwiseNullaryOp.h
index 723340cef..caa86fa97 100644
--- a/Eigen/src/Core/CwiseNullaryOp.h
+++ b/Eigen/src/Core/CwiseNullaryOp.h
@@ -60,11 +60,7 @@ struct ei_traits<CwiseNullaryOp<NullaryOp, MatrixType> >
 
 template<typename NullaryOp, typename MatrixType>
 class CwiseNullaryOp : ei_no_assignment_operator,
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   public MatrixBase<CwiseNullaryOp<NullaryOp, MatrixType> >
-#else
-  public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/CwiseUnaryOp.h b/Eigen/src/Core/CwiseUnaryOp.h
index a6577a31e..a50a9c30d 100644
--- a/Eigen/src/Core/CwiseUnaryOp.h
+++ b/Eigen/src/Core/CwiseUnaryOp.h
@@ -63,11 +63,7 @@ struct ei_traits<CwiseUnaryOp<UnaryOp, MatrixType> >
 
 template<typename UnaryOp, typename MatrixType>
 class CwiseUnaryOp : ei_no_assignment_operator,
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   public MatrixBase<CwiseUnaryOp<UnaryOp, MatrixType> >
-#else
-  public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/DiagonalCoeffs.h b/Eigen/src/Core/DiagonalCoeffs.h
index 83a11807e..21ca015d2 100644
--- a/Eigen/src/Core/DiagonalCoeffs.h
+++ b/Eigen/src/Core/DiagonalCoeffs.h
@@ -60,11 +60,7 @@ struct ei_traits<DiagonalCoeffs<MatrixType> >
 };
 
 template<typename MatrixType> class DiagonalCoeffs
-#ifndef EIGEN_PARSED_BY_DOXYGEN
    : public MatrixBase<DiagonalCoeffs<MatrixType> >
-#else
-  : public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/DiagonalMatrix.h b/Eigen/src/Core/DiagonalMatrix.h
index da7bf2dd4..06507dc68 100644
--- a/Eigen/src/Core/DiagonalMatrix.h
+++ b/Eigen/src/Core/DiagonalMatrix.h
@@ -56,11 +56,7 @@ struct ei_traits<DiagonalMatrix<CoeffsVectorType> >
 
 template<typename CoeffsVectorType>
 class DiagonalMatrix : ei_no_assignment_operator,
-#ifndef EIGEN_PARSED_BY_DOXYGEN
    public MatrixBase<DiagonalMatrix<CoeffsVectorType> >
-#else
-  public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/DiagonalProduct.h b/Eigen/src/Core/DiagonalProduct.h
index 83ca8d1b3..4ee3c46c3 100644
--- a/Eigen/src/Core/DiagonalProduct.h
+++ b/Eigen/src/Core/DiagonalProduct.h
@@ -61,11 +61,7 @@ struct ei_traits<Product<LhsNested, RhsNested, DiagonalProduct> >
 };
 
 template<typename LhsNested, typename RhsNested> class Product<LhsNested, RhsNested, DiagonalProduct> : ei_no_assignment_operator,
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   public MatrixBase<Product<LhsNested, RhsNested, DiagonalProduct> >
-#else
-  public MatrixBase
-#endif
 {
     typedef typename ei_traits<Product>::_LhsNested _LhsNested;
     typedef typename ei_traits<Product>::_RhsNested _RhsNested;
diff --git a/Eigen/src/Core/Flagged.h b/Eigen/src/Core/Flagged.h
index 4dbcbd56d..a6abe617b 100644
--- a/Eigen/src/Core/Flagged.h
+++ b/Eigen/src/Core/Flagged.h
@@ -55,11 +55,7 @@ struct ei_traits<Flagged<ExpressionType, Added, Removed> >
 };
 
 template<typename ExpressionType, unsigned int Added, unsigned int Removed> class Flagged
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MatrixBase<Flagged<ExpressionType, Added, Removed> >
-#else
-  : public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/Map.h b/Eigen/src/Core/Map.h
index 4da6b942a..7dfaac273 100644
--- a/Eigen/src/Core/Map.h
+++ b/Eigen/src/Core/Map.h
@@ -57,11 +57,7 @@ struct ei_traits<Map<MatrixType, _PacketAccess> > : public ei_traits<MatrixType>
 };
 
 template<typename MatrixType, int PacketAccess> class Map
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MapBase<Map<MatrixType, PacketAccess> >
-#else
-  : public MapBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/Matrix.h b/Eigen/src/Core/Matrix.h
index 4fce434e9..44e4c45b8 100644
--- a/Eigen/src/Core/Matrix.h
+++ b/Eigen/src/Core/Matrix.h
@@ -97,11 +97,7 @@ struct ei_traits<Matrix<_Scalar, _Rows, _Cols, _StorageOrder, _MaxRows, _MaxCols
 
 template<typename _Scalar, int _Rows, int _Cols, int _StorageOrder, int _MaxRows, int _MaxCols>
 class Matrix
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MatrixBase<Matrix<_Scalar, _Rows, _Cols, _StorageOrder, _MaxRows, _MaxCols> >
-#else
-  : public MatrixBase
-#endif
 {
   public:
     EIGEN_GENERIC_PUBLIC_INTERFACE(Matrix)
diff --git a/Eigen/src/Core/Minor.h b/Eigen/src/Core/Minor.h
index 70e358741..9e87c9b9b 100644
--- a/Eigen/src/Core/Minor.h
+++ b/Eigen/src/Core/Minor.h
@@ -58,11 +58,7 @@ struct ei_traits<Minor<MatrixType> >
 };
 
 template<typename MatrixType> class Minor
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MatrixBase<Minor<MatrixType> >
-#else
-  : public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/NestByValue.h b/Eigen/src/Core/NestByValue.h
index 198e9df78..86d8795cd 100644
--- a/Eigen/src/Core/NestByValue.h
+++ b/Eigen/src/Core/NestByValue.h
@@ -52,11 +52,7 @@ struct ei_traits<NestByValue<ExpressionType> >
 };
 
 template<typename ExpressionType> class NestByValue
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MatrixBase<NestByValue<ExpressionType> >
-#else
-  : public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/Part.h b/Eigen/src/Core/Part.h
index 61c8507ef..4d39c4c08 100644
--- a/Eigen/src/Core/Part.h
+++ b/Eigen/src/Core/Part.h
@@ -59,11 +59,7 @@ struct ei_traits<Part<MatrixType, Mode> >
 };
 
 template<typename MatrixType, unsigned int Mode> class Part
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MatrixBase<Part<MatrixType, Mode> >
-#else
-  : public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/Product.h b/Eigen/src/Core/Product.h
index 3132d4e46..f18bc1e4a 100644
--- a/Eigen/src/Core/Product.h
+++ b/Eigen/src/Core/Product.h
@@ -168,11 +168,7 @@ struct ei_traits<Product<LhsNested, RhsNested, ProductMode> >
 };
 
 template<typename LhsNested, typename RhsNested, int ProductMode> class Product : ei_no_assignment_operator,
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   public MatrixBase<Product<LhsNested, RhsNested, ProductMode> >
-#else
-  public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/Swap.h b/Eigen/src/Core/Swap.h
index f1918c12b..835fa61b2 100644
--- a/Eigen/src/Core/Swap.h
+++ b/Eigen/src/Core/Swap.h
@@ -46,11 +46,7 @@ struct ei_traits<SwapWrapper<ExpressionType> >
 };
 
 template<typename ExpressionType> class SwapWrapper
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MatrixBase<SwapWrapper<ExpressionType> >
-#else
-  : public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Core/Transpose.h b/Eigen/src/Core/Transpose.h
index 5f8b263da..dba19f025 100644
--- a/Eigen/src/Core/Transpose.h
+++ b/Eigen/src/Core/Transpose.h
@@ -57,11 +57,7 @@ struct ei_traits<Transpose<MatrixType> >
 };
 
 template<typename MatrixType> class Transpose
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public MatrixBase<Transpose<MatrixType> >
-#else
-  : public MatrixBase
-#endif
 {
   public:
 
diff --git a/Eigen/src/Sparse/HashMatrix.h b/Eigen/src/Sparse/HashMatrix.h
index 47c673c61..1d6d33cce 100644
--- a/Eigen/src/Sparse/HashMatrix.h
+++ b/Eigen/src/Sparse/HashMatrix.h
@@ -43,11 +43,7 @@ struct ei_traits<HashMatrix<_Scalar, _Flags> >
 // TODO reimplement this class using custom linked lists
 template<typename _Scalar, int _Flags>
 class HashMatrix
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public SparseMatrixBase<HashMatrix<_Scalar, _Flags> >
-#else
-  : public SparseMatrixBase
-#endif
 {
   public:
     EIGEN_GENERIC_PUBLIC_INTERFACE(HashMatrix)
diff --git a/Eigen/src/Sparse/LinkedVectorMatrix.h b/Eigen/src/Sparse/LinkedVectorMatrix.h
index 2ffb1d930..dc34aced6 100644
--- a/Eigen/src/Sparse/LinkedVectorMatrix.h
+++ b/Eigen/src/Sparse/LinkedVectorMatrix.h
@@ -53,11 +53,7 @@ struct LinkedVectorChunk
 
 template<typename _Scalar, int _Flags>
 class LinkedVectorMatrix
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public SparseMatrixBase<LinkedVectorMatrix<_Scalar,_Flags> >
-#else
-  : public SparseMatrixBase
-#endif
 {
   public:
     EIGEN_GENERIC_PUBLIC_INTERFACE(LinkedVectorMatrix)
diff --git a/Eigen/src/Sparse/SparseMatrix.h b/Eigen/src/Sparse/SparseMatrix.h
index acf0e10b2..9d4f325a3 100644
--- a/Eigen/src/Sparse/SparseMatrix.h
+++ b/Eigen/src/Sparse/SparseMatrix.h
@@ -53,11 +53,7 @@ struct ei_traits<SparseMatrix<_Scalar, _Flags> >
 
 template<typename _Scalar, int _Flags>
 class SparseMatrix
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   : public SparseMatrixBase<SparseMatrix<_Scalar, _Flags> >
-#else
-  : public SparseMatrixBase
-#endif
 {
   public:
     EIGEN_GENERIC_PUBLIC_INTERFACE(SparseMatrix)
diff --git a/Eigen/src/Sparse/SparseProduct.h b/Eigen/src/Sparse/SparseProduct.h
index b19cb87da..7be5ecefd 100644
--- a/Eigen/src/Sparse/SparseProduct.h
+++ b/Eigen/src/Sparse/SparseProduct.h
@@ -88,11 +88,7 @@ struct ei_traits<Product<LhsNested, RhsNested, SparseProduct> >
 };
 
 template<typename LhsNested, typename RhsNested> class Product<LhsNested,RhsNested,SparseProduct> : ei_no_assignment_operator,
-#ifndef EIGEN_PARSED_BY_DOXYGEN
   public MatrixBase<Product<LhsNested, RhsNested, SparseProduct> >
-#else
-  public MatrixBase
-#endif
 {
   public:
 
diff --git a/Mainpage.dox b/Mainpage.dox
index eee01f8c4..e036a8283 100644
--- a/Mainpage.dox
+++ b/Mainpage.dox
@@ -14,6 +14,6 @@ In order to generate the documentation of Eigen, please follow these steps:
 After doing that, you will find the HTML documentation in the doc/html/ subdirectory of the build directory.
 
 <h2>Note however that the documentation is available online here:
-<a href="http://eigen.tuxfamily.org/api/">http://eigen.tuxfamily.org/api</a>
+<a href="http://eigen.tuxfamily.org/api/">http://eigen.tuxfamily.org/api</a></h2>
 
 */
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index e2a31978c..c8693af84 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -38,6 +38,7 @@ ADD_CUSTOM_TARGET(
                                    ${CMAKE_CURRENT_BINARY_DIR}/html/
   COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/buildexamplelist.sh ${CMAKE_SOURCE_DIR} > ${CMAKE_CURRENT_BINARY_DIR}/ExampleList.dox
   COMMAND doxygen
+  COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/cleanhierarchy.sh ${CMAKE_CURRENT_BINARY_DIR}/html/hierarchy.html
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 )
 
diff --git a/doc/QuickStartGuide.dox b/doc/QuickStartGuide.dox
index a2fe4f23d..d8a58b208 100644
--- a/doc/QuickStartGuide.dox
+++ b/doc/QuickStartGuide.dox
@@ -188,7 +188,7 @@ MatrixXi mat2x2 = Map<MatrixXi>(data,2,2);
 
 
 \subsection TutorialCommaInit Comma initializer
-Eigen also offer a \link MatrixBase::operator<<(const Scalar &) comma initializer syntax \endlink which allows you to set all the coefficients of a matrix to specific values:
+Eigen also offer a \ref MatrixBaseCommaInitRef "comma initializer syntax" which allows you to set all the coefficients of a matrix to specific values:
 <table class="tutorial_code"><tr><td>
 \include Tutorial_commainit_01.cpp
 </td>
@@ -295,8 +295,7 @@ etc.
 <td><table class="tutorial_code">
 <tr><td>
 \b Trigo: \n
-\link Cwise::sin sin \endlink, \link Cwise::cos cos \endlink,
-\link Cwise::tan tan \endlink</td><td>\code
+\link Cwise::sin sin \endlink, \link Cwise::cos cos \endlink</td><td>\code
 mat3 = mat1.cwise().sin();
 etc.
 \endcode
@@ -538,7 +537,7 @@ more compact, fast and stable. AngleAxis are only useful to create other rotatio
 
 \subsection TutorialGeoCommonRotationAPI Common API across rotation types
 
-To some extent, Eigen's \ref Geometry_Module "geometry module" allows you to write
+To some extent, Eigen's \ref GeometryModule "geometry module" allows you to write
 generic algorithms working on both 2D and 3D rotations of any of the five above types.
 The following operation are supported:
 <table class="tutorial_code">
diff --git a/doc/cleanhierarchy.sh b/doc/cleanhierarchy.sh
new file mode 100755
index 000000000..892cf393c
--- /dev/null
+++ b/doc/cleanhierarchy.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+
+sed -i 's/^.li.*MatrixBase\&lt.*gt.*a.$/ /g' $1
+sed -i 's/^.li.*MapBase\&lt.*gt.*a.$/ /g' $1