Various documentation improvements.

* Add short documentation for Array class
* Put all classes explicitly in Core module (where applicable)
* Section on Modules in Quick Reference Guide
* Put Page 7 after Page 6 in Contents :)

42 files changed, 63 insertions, 1 deletions

diff --git a/Eigen/src/Core/Array.h b/Eigen/src/Core/Array.h
index 0a9366254..61e1950eb 100644
--- a/Eigen/src/Core/Array.h
+++ b/Eigen/src/Core/Array.h
@@ -25,6 +25,20 @@
 #ifndef EIGEN_ARRAY_H
 #define EIGEN_ARRAY_H
 
+/** \class Array 
+  * \ingroup Core_Module
+  *
+  * \brief General-purpose arrays with easy API for coefficient-wise operations
+  *
+  * The %Array class is very similar to the Matrix class. It provides
+  * general-purpose one- and two-dimensional arrays. The difference between the
+  * %Array and the %Matrix class is primarily in the API: the API for the
+  * %Array class provides easy access to coefficient-wise operations, while the
+  * API for the %Matrix class provides easy access to linear-algebra
+  * operations.
+  *
+  * \sa \ref TutorialArrayClass
+  */
 template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
 struct ei_traits<Array<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> > : ei_traits<Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols> >
 {
@@ -231,6 +245,7 @@ class Array
 };
 
 /** \defgroup arraytypedefs Global array typedefs
+  * \ingroup Core_Module
   *
   * Eigen defines several typedef shortcuts for most common 1D and 2D array types.
   *
diff --git a/Eigen/src/Core/ArrayBase.h b/Eigen/src/Core/ArrayBase.h
index 20782e2cf..1a54b2335 100644
--- a/Eigen/src/Core/ArrayBase.h
+++ b/Eigen/src/Core/ArrayBase.h
@@ -28,6 +28,7 @@
 template<typename ExpressionType> class MatrixWrapper;
 
 /** \class ArrayBase
+  * \ingroup Core_Module
   *
   * \brief Base class for all 1D and 2D array, and related expressions
   *
diff --git a/Eigen/src/Core/ArrayWrapper.h b/Eigen/src/Core/ArrayWrapper.h
index d4b7c45c0..dc5bba443 100644
--- a/Eigen/src/Core/ArrayWrapper.h
+++ b/Eigen/src/Core/ArrayWrapper.h
@@ -26,6 +26,7 @@
 #define EIGEN_ARRAYWRAPPER_H
 
 /** \class ArrayWrapper
+  * \ingroup Core_Module
   *
   * \brief Expression of a mathematical vector or matrix as an array object
   *
@@ -110,6 +111,7 @@ class ArrayWrapper : public ArrayBase<ArrayWrapper<ExpressionType> >
 };
 
 /** \class MatrixWrapper
+  * \ingroup Core_Module
   *
   * \brief Expression of an array as a mathematical vector or matrix
   *
diff --git a/Eigen/src/Core/BandMatrix.h b/Eigen/src/Core/BandMatrix.h
index 51b38aa7f..e846b38e5 100644
--- a/Eigen/src/Core/BandMatrix.h
+++ b/Eigen/src/Core/BandMatrix.h
@@ -27,6 +27,7 @@
 
 /**
   * \class BandMatrix
+  * \ingroup Core_Module
   *
   * \brief Represents a rectangular matrix with a banded storage
   *
@@ -205,6 +206,7 @@ class BandMatrix : public EigenBase<BandMatrix<_Scalar,Rows,Cols,Supers,Subs,Opt
 
 /**
   * \class TridiagonalMatrix
+  * \ingroup Core_Module
   *
   * \brief Represents a tridiagonal matrix
   *
diff --git a/Eigen/src/Core/Block.h b/Eigen/src/Core/Block.h
index 79f1d738d..f888d5ea0 100644
--- a/Eigen/src/Core/Block.h
+++ b/Eigen/src/Core/Block.h
@@ -27,6 +27,7 @@
 #define EIGEN_BLOCK_H
 
 /** \class Block
+  * \ingroup Core_Module
   *
   * \brief Expression of a fixed-size or dynamic-size block
   *
diff --git a/Eigen/src/Core/CommaInitializer.h b/Eigen/src/Core/CommaInitializer.h
index 2b09e9daa..da8df5592 100644
--- a/Eigen/src/Core/CommaInitializer.h
+++ b/Eigen/src/Core/CommaInitializer.h
@@ -27,6 +27,7 @@
 #define EIGEN_COMMAINITIALIZER_H
 
 /** \class CommaInitializer
+  * \ingroup Core_Module
   *
   * \brief Helper class used by the comma initializer operator
   *
diff --git a/Eigen/src/Core/CwiseBinaryOp.h b/Eigen/src/Core/CwiseBinaryOp.h
index 2639c5f8d..7f4587b53 100644
--- a/Eigen/src/Core/CwiseBinaryOp.h
+++ b/Eigen/src/Core/CwiseBinaryOp.h
@@ -27,6 +27,7 @@
 #define EIGEN_CWISE_BINARY_OP_H
 
 /** \class CwiseBinaryOp
+  * \ingroup Core_Module
   *
   * \brief Generic expression where a coefficient-wise binary operator is applied to two expressions
   *
diff --git a/Eigen/src/Core/CwiseNullaryOp.h b/Eigen/src/Core/CwiseNullaryOp.h
index f053ddc90..25041d1b7 100644
--- a/Eigen/src/Core/CwiseNullaryOp.h
+++ b/Eigen/src/Core/CwiseNullaryOp.h
@@ -26,6 +26,7 @@
 #define EIGEN_CWISE_NULLARY_OP_H
 
 /** \class CwiseNullaryOp
+  * \ingroup Core_Module
   *
   * \brief Generic expression of a matrix where all coefficients are defined by a functor
   *
diff --git a/Eigen/src/Core/CwiseUnaryOp.h b/Eigen/src/Core/CwiseUnaryOp.h
index b5cdf22a2..4c92f36bb 100644
--- a/Eigen/src/Core/CwiseUnaryOp.h
+++ b/Eigen/src/Core/CwiseUnaryOp.h
@@ -27,6 +27,7 @@
 #define EIGEN_CWISE_UNARY_OP_H
 
 /** \class CwiseUnaryOp
+  * \ingroup Core_Module
   *
   * \brief Generic expression where a coefficient-wise unary operator is applied to an expression
   *
diff --git a/Eigen/src/Core/CwiseUnaryView.h b/Eigen/src/Core/CwiseUnaryView.h
index 3888b86b2..612b28f1f 100644
--- a/Eigen/src/Core/CwiseUnaryView.h
+++ b/Eigen/src/Core/CwiseUnaryView.h
@@ -26,6 +26,7 @@
 #define EIGEN_CWISE_UNARY_VIEW_H
 
 /** \class CwiseUnaryView
+  * \ingroup Core_Module
   *
   * \brief Generic lvalue expression of a coefficient-wise unary operator of a matrix or a vector
   *
diff --git a/Eigen/src/Core/DenseBase.h b/Eigen/src/Core/DenseBase.h
index f45af7e97..8c1e24fec 100644
--- a/Eigen/src/Core/DenseBase.h
+++ b/Eigen/src/Core/DenseBase.h
@@ -27,6 +27,7 @@
 #define EIGEN_DENSEBASE_H
 
 /** \class DenseBase
+  * \ingroup Core_Module
   *
   * \brief Base class for all dense matrices, vectors, and arrays
   *
diff --git a/Eigen/src/Core/Diagonal.h b/Eigen/src/Core/Diagonal.h
index b72ce93fa..512e93883 100644
--- a/Eigen/src/Core/Diagonal.h
+++ b/Eigen/src/Core/Diagonal.h
@@ -26,6 +26,7 @@
 #define EIGEN_DIAGONAL_H
 
 /** \class Diagonal
+  * \ingroup Core_Module
   *
   * \brief Expression of a diagonal/subdiagonal/superdiagonal in a matrix
   *
diff --git a/Eigen/src/Core/DiagonalMatrix.h b/Eigen/src/Core/DiagonalMatrix.h
index c4391819a..8c4200a6f 100644
--- a/Eigen/src/Core/DiagonalMatrix.h
+++ b/Eigen/src/Core/DiagonalMatrix.h
@@ -87,6 +87,7 @@ void DiagonalBase<Derived>::evalTo(MatrixBase<DenseDerived> &other) const
 #endif
 
 /** \class DiagonalMatrix
+  * \ingroup Core_Module
   *
   * \brief Represents a diagonal matrix with its storage
   *
@@ -188,6 +189,7 @@ class DiagonalMatrix
 };
 
 /** \class DiagonalWrapper
+  * \ingroup Core_Module
   *
   * \brief Expression of a diagonal matrix
   *
diff --git a/Eigen/src/Core/Flagged.h b/Eigen/src/Core/Flagged.h
index 7936f9dcf..9211c50e8 100644
--- a/Eigen/src/Core/Flagged.h
+++ b/Eigen/src/Core/Flagged.h
@@ -26,6 +26,7 @@
 #define EIGEN_FLAGGED_H
 
 /** \class Flagged
+  * \ingroup Core_Module
   *
   * \brief Expression with modified flags
   *
diff --git a/Eigen/src/Core/ForceAlignedAccess.h b/Eigen/src/Core/ForceAlignedAccess.h
index 114d7bf97..06d78fbe2 100644
--- a/Eigen/src/Core/ForceAlignedAccess.h
+++ b/Eigen/src/Core/ForceAlignedAccess.h
@@ -26,6 +26,7 @@
 #define EIGEN_FORCEALIGNEDACCESS_H
 
 /** \class ForceAlignedAccess
+  * \ingroup Core_Module
   *
   * \brief Enforce aligned packet loads and stores regardless of what is requested
   *
diff --git a/Eigen/src/Core/IO.h b/Eigen/src/Core/IO.h
index 7a823d225..7c742d867 100644
--- a/Eigen/src/Core/IO.h
+++ b/Eigen/src/Core/IO.h
@@ -31,6 +31,7 @@ enum { StreamPrecision = -1,
        FullPrecision = -2 };
 
 /** \class IOFormat
+  * \ingroup Core_Module
   *
   * \brief Stores a set of parameters controlling the way matrices are printed
   *
@@ -80,6 +81,7 @@ struct IOFormat
 };
 
 /** \class WithFormat
+  * \ingroup Core_Module
   *
   * \brief Pseudo expression providing matrix output with given format
   *
diff --git a/Eigen/src/Core/Map.h b/Eigen/src/Core/Map.h
index 0c4d08a17..3386c6d69 100644
--- a/Eigen/src/Core/Map.h
+++ b/Eigen/src/Core/Map.h
@@ -27,6 +27,7 @@
 #define EIGEN_MAP_H
 
 /** \class Map
+  * \ingroup Core_Module
   *
   * \brief A matrix or vector expression mapping an existing array of data.
   *
diff --git a/Eigen/src/Core/MapBase.h b/Eigen/src/Core/MapBase.h
index 4dfa8f82d..6af7bb793 100644
--- a/Eigen/src/Core/MapBase.h
+++ b/Eigen/src/Core/MapBase.h
@@ -27,6 +27,7 @@
 #define EIGEN_MAPBASE_H
 
 /** \class MapBase
+  * \ingroup Core_Module
   *
   * \brief Base class for Map and Block expression with direct access
   *
diff --git a/Eigen/src/Core/Matrix.h b/Eigen/src/Core/Matrix.h
index 726969720..1c9d32a29 100644
--- a/Eigen/src/Core/Matrix.h
+++ b/Eigen/src/Core/Matrix.h
@@ -27,6 +27,7 @@
 #define EIGEN_MATRIX_H
 
 /** \class Matrix
+  * \ingroup Core_Module
   *
   * \brief The matrix class, also used for vectors and row-vectors
   *
diff --git a/Eigen/src/Core/MatrixBase.h b/Eigen/src/Core/MatrixBase.h
index 94ddb8691..0c2bbf5bf 100644
--- a/Eigen/src/Core/MatrixBase.h
+++ b/Eigen/src/Core/MatrixBase.h
@@ -27,6 +27,7 @@
 #define EIGEN_MATRIXBASE_H
 
 /** \class MatrixBase
+  * \ingroup Core_Module
   *
   * \brief Base class for all dense matrices, vectors, and expressions
   *
diff --git a/Eigen/src/Core/MatrixStorage.h b/Eigen/src/Core/MatrixStorage.h
index 5dc8640c0..c6e7e20b2 100644
--- a/Eigen/src/Core/MatrixStorage.h
+++ b/Eigen/src/Core/MatrixStorage.h
@@ -79,6 +79,7 @@ struct ei_matrix_array<T, 0, MatrixOptions, Alignment>
 /** \internal
   *
   * \class ei_matrix_storage
+  * \ingroup Core_Module
   *
   * \brief Stores the data of a matrix
   *
diff --git a/Eigen/src/Core/NestByValue.h b/Eigen/src/Core/NestByValue.h
index f01e1e38d..885002e26 100644
--- a/Eigen/src/Core/NestByValue.h
+++ b/Eigen/src/Core/NestByValue.h
@@ -27,6 +27,7 @@
 #define EIGEN_NESTBYVALUE_H
 
 /** \class NestByValue
+  * \ingroup Core_Module
   *
   * \brief Expression which must be nested by value
   *
diff --git a/Eigen/src/Core/NoAlias.h b/Eigen/src/Core/NoAlias.h
index ac889c565..d34f83b7b 100644
--- a/Eigen/src/Core/NoAlias.h
+++ b/Eigen/src/Core/NoAlias.h
@@ -26,6 +26,7 @@
 #define EIGEN_NOALIAS_H
 
 /** \class NoAlias
+  * \ingroup Core_Module
   *
   * \brief Pseudo expression providing an operator = assuming no aliasing
   *
diff --git a/Eigen/src/Core/NumTraits.h b/Eigen/src/Core/NumTraits.h
index a0ffa4645..9e6e35a04 100644
--- a/Eigen/src/Core/NumTraits.h
+++ b/Eigen/src/Core/NumTraits.h
@@ -26,6 +26,7 @@
 #define EIGEN_NUMTRAITS_H
 
 /** \class NumTraits
+  * \ingroup Core_Module
   *
   * \brief Holds information about the various numeric (i.e. scalar) types allowed by Eigen.
   *
diff --git a/Eigen/src/Core/PermutationMatrix.h b/Eigen/src/Core/PermutationMatrix.h
index 1b212efd7..afe37ef6d 100644
--- a/Eigen/src/Core/PermutationMatrix.h
+++ b/Eigen/src/Core/PermutationMatrix.h
@@ -27,6 +27,7 @@
 #define EIGEN_PERMUTATIONMATRIX_H
 
 /** \class PermutationMatrix
+  * \ingroup Core_Module
   *
   * \brief Permutation matrix
   *
diff --git a/Eigen/src/Core/Product.h b/Eigen/src/Core/Product.h
index 707b6ec85..66435e0e3 100644
--- a/Eigen/src/Core/Product.h
+++ b/Eigen/src/Core/Product.h
@@ -27,6 +27,7 @@
 #define EIGEN_PRODUCT_H
 
 /** \class GeneralProduct
+  * \ingroup Core_Module
   *
   * \brief Expression of the product of two general matrices or vectors
   *
@@ -120,6 +121,7 @@ template<>              struct ei_product_type_selector<Small,Large,Small>  { en
 template<>              struct ei_product_type_selector<Large,Large,Small>  { enum { ret = GemmProduct }; };
 
 /** \class ProductReturnType
+  * \ingroup Core_Module
   *
   * \brief Helper class to get the correct and optimized returned type of operator*
   *
diff --git a/Eigen/src/Core/ProductBase.h b/Eigen/src/Core/ProductBase.h
index 8f8052756..b3504f9d0 100644
--- a/Eigen/src/Core/ProductBase.h
+++ b/Eigen/src/Core/ProductBase.h
@@ -26,6 +26,7 @@
 #define EIGEN_PRODUCTBASE_H
 
 /** \class ProductBase
+  * \ingroup Core_Module
   *
   */
 template<typename Derived, typename _Lhs, typename _Rhs>
diff --git a/Eigen/src/Core/Replicate.h b/Eigen/src/Core/Replicate.h
index 23f02c2d9..87dea0533 100644
--- a/Eigen/src/Core/Replicate.h
+++ b/Eigen/src/Core/Replicate.h
@@ -27,6 +27,7 @@
 
 /**
   * \class Replicate
+  * \ingroup Core_Module
   *
   * \brief Expression of the multiple replication of a matrix or vector
   *
diff --git a/Eigen/src/Core/ReturnByValue.h b/Eigen/src/Core/ReturnByValue.h
index 52326b0e1..82f194b56 100644
--- a/Eigen/src/Core/ReturnByValue.h
+++ b/Eigen/src/Core/ReturnByValue.h
@@ -27,6 +27,7 @@
 #define EIGEN_RETURNBYVALUE_H
 
 /** \class ReturnByValue
+  * \ingroup Core_Module
   *
   */
 template<typename Derived>
diff --git a/Eigen/src/Core/Reverse.h b/Eigen/src/Core/Reverse.h
index a581d9f27..5a96aeeb3 100644
--- a/Eigen/src/Core/Reverse.h
+++ b/Eigen/src/Core/Reverse.h
@@ -28,6 +28,7 @@
 #define EIGEN_REVERSE_H
 
 /** \class Reverse
+  * \ingroup Core_Module
   *
   * \brief Expression of the reverse of a vector or matrix
   *
diff --git a/Eigen/src/Core/Select.h b/Eigen/src/Core/Select.h
index f5f220bff..000c70905 100644
--- a/Eigen/src/Core/Select.h
+++ b/Eigen/src/Core/Select.h
@@ -26,6 +26,7 @@
 #define EIGEN_SELECT_H
 
 /** \class Select
+  * \ingroup Core_Module
   *
   * \brief Expression of a coefficient wise version of the C++ ternary operator ?:
   *
diff --git a/Eigen/src/Core/SelfAdjointView.h b/Eigen/src/Core/SelfAdjointView.h
index dadea9c09..bb8ab168d 100644
--- a/Eigen/src/Core/SelfAdjointView.h
+++ b/Eigen/src/Core/SelfAdjointView.h
@@ -26,6 +26,7 @@
 #define EIGEN_SELFADJOINTMATRIX_H
 
 /** \class SelfAdjointView
+  * \ingroup Core_Module
   *
   *
   * \brief Expression of a selfadjoint matrix from a triangular part of a dense matrix
diff --git a/Eigen/src/Core/SelfCwiseBinaryOp.h b/Eigen/src/Core/SelfCwiseBinaryOp.h
index fbeb5bff2..acdbb8658 100644
--- a/Eigen/src/Core/SelfCwiseBinaryOp.h
+++ b/Eigen/src/Core/SelfCwiseBinaryOp.h
@@ -26,6 +26,7 @@
 #define EIGEN_SELFCWISEBINARYOP_H
 
 /** \class SelfCwiseBinaryOp
+  * \ingroup Core_Module
   *
   * \internal
   *
diff --git a/Eigen/src/Core/Stride.h b/Eigen/src/Core/Stride.h
index 5f9a18523..47515b548 100644
--- a/Eigen/src/Core/Stride.h
+++ b/Eigen/src/Core/Stride.h
@@ -26,6 +26,7 @@
 #define EIGEN_STRIDE_H
 
 /** \class Stride
+  * \ingroup Core_Module
   *
   * \brief Holds strides information for Map
   *
diff --git a/Eigen/src/Core/Swap.h b/Eigen/src/Core/Swap.h
index 8e5994aa9..086d7f32c 100644
--- a/Eigen/src/Core/Swap.h
+++ b/Eigen/src/Core/Swap.h
@@ -26,6 +26,7 @@
 #define EIGEN_SWAP_H
 
 /** \class SwapWrapper
+  * \ingroup Core_Module
   *
   * \internal
   *
diff --git a/Eigen/src/Core/Transpose.h b/Eigen/src/Core/Transpose.h
index f9c82fb77..3a84b84ff 100644
--- a/Eigen/src/Core/Transpose.h
+++ b/Eigen/src/Core/Transpose.h
@@ -27,6 +27,7 @@
 #define EIGEN_TRANSPOSE_H
 
 /** \class Transpose
+  * \ingroup Core_Module
   *
   * \brief Expression of the transpose of a matrix
   *
diff --git a/Eigen/src/Core/Transpositions.h b/Eigen/src/Core/Transpositions.h
index 012b74159..6703b1e58 100644
--- a/Eigen/src/Core/Transpositions.h
+++ b/Eigen/src/Core/Transpositions.h
@@ -26,6 +26,7 @@
 #define EIGEN_TRANSPOSITIONS_H
 
 /** \class Transpositions
+  * \ingroup Core_Module
   *
   * \brief Represents a sequence of transpositions (row/column interchange)
   *
diff --git a/Eigen/src/Core/TriangularMatrix.h b/Eigen/src/Core/TriangularMatrix.h
index 99e8e426c..c66bbb9fa 100644
--- a/Eigen/src/Core/TriangularMatrix.h
+++ b/Eigen/src/Core/TriangularMatrix.h
@@ -29,6 +29,7 @@
 /** \internal
   *
   * \class TriangularBase
+  * \ingroup Core_Module
   *
   * \brief Base class for triangular part in a matrix
   */
@@ -112,6 +113,7 @@ template<typename Derived> class TriangularBase : public EigenBase<Derived>
 };
 
 /** \class TriangularView
+  * \ingroup Core_Module
   *
   * \brief Base class for triangular part in a matrix
   *
diff --git a/Eigen/src/Core/VectorBlock.h b/Eigen/src/Core/VectorBlock.h
index 1840095cf..84040bca1 100644
--- a/Eigen/src/Core/VectorBlock.h
+++ b/Eigen/src/Core/VectorBlock.h
@@ -27,6 +27,7 @@
 #define EIGEN_VECTORBLOCK_H
 
 /** \class VectorBlock
+  * \ingroup Core_Module
   *
   * \brief Expression of a fixed-size or dynamic-size sub-vector
   *
diff --git a/Eigen/src/Core/VectorwiseOp.h b/Eigen/src/Core/VectorwiseOp.h
index 93373b49b..1867961f5 100644
--- a/Eigen/src/Core/VectorwiseOp.h
+++ b/Eigen/src/Core/VectorwiseOp.h
@@ -27,6 +27,7 @@
 #define EIGEN_PARTIAL_REDUX_H
 
 /** \class PartialReduxExpr
+  * \ingroup Core_Module
   *
   * \brief Generic expression of a partially reduxed matrix
   *
@@ -154,6 +155,7 @@ struct ei_member_redux {
 };
 
 /** \class VectorwiseOp
+  * \ingroup Core_Module
   *
   * \brief Pseudo expression providing partial reduction operations
   *
diff --git a/Eigen/src/Core/util/Constants.h b/Eigen/src/Core/util/Constants.h
index 0c24d2fa9..d758c2a0b 100644
--- a/Eigen/src/Core/util/Constants.h
+++ b/Eigen/src/Core/util/Constants.h
@@ -38,7 +38,7 @@ const int Dynamic = -1;
   */
 const int Infinity = -1;
 
-/** \defgroup flags flags
+/** \defgroup flags Flags
   * \ingroup Core_Module
   *
   * These are the possible bits which can be OR'ed to constitute the flags of a matrix or
diff --git a/Eigen/src/Core/util/Memory.h b/Eigen/src/Core/util/Memory.h
index 21ea45a24..1b89525a8 100644
--- a/Eigen/src/Core/util/Memory.h
+++ b/Eigen/src/Core/util/Memory.h
@@ -495,6 +495,7 @@ inline static Index ei_first_aligned(const Scalar* array, Index size)
 /****************************************************************************/
 
 /** \class aligned_allocator
+* \ingroup Core_Module
 *
 * \brief STL compatible allocator to use with with 16 byte aligned types
 *