Several changes in comments to keep Doxygen happy.

Eigen/src/Core/Array.h

@@ -266,7 +266,7 @@ class Array
 #define EIGEN_MAKE_ARRAY_TYPEDEFS(Type, TypeSuffix, Size, SizeSuffix)   \
 /** \ingroup arraytypedefs */                                    \
 typedef Array<Type, Size, Size> Array##SizeSuffix##SizeSuffix##TypeSuffix;  \
-/** \ingroup matrixtypedefs */                                    \
+/** \ingroup arraytypedefs */                                    \
 typedef Array<Type, Size, 1>    Array##SizeSuffix##TypeSuffix;
 
 #define EIGEN_MAKE_ARRAY_FIXED_TYPEDEFS(Type, TypeSuffix, Size)         \

Eigen/src/Core/CwiseNullaryOp.h

@@ -251,7 +251,7 @@ DenseBase<Derived>::LinSpaced(Sequential_t, Index size, const Scalar& low, const
 }
 
 /**
-  * \copydoc DenseBase<Derived>::LinSpaced(Sequential_t, Index, const Scalar&, const Scalar&)
+  * \copydoc DenseBase::LinSpaced(Sequential_t, Index, const Scalar&, const Scalar&)
   * Special version for fixed size types which does not require the size parameter.
   */
 template<typename Derived>
@@ -284,7 +284,7 @@ DenseBase<Derived>::LinSpaced(Index size, const Scalar& low, const Scalar& high)
 }
 
 /**
-  * \copydoc DenseBase<Derived>::LinSpaced(Index, const Scalar&, const Scalar&)
+  * \copydoc DenseBase::LinSpaced(Index, const Scalar&, const Scalar&)
   * Special version for fixed size types which does not require the size parameter.
   */
 template<typename Derived>
@@ -359,6 +359,7 @@ DenseStorageBase<Derived>::setConstant(Index size, const Scalar& value)
   *
   * \param rows the new number of rows
   * \param cols the new number of columns
+  * \param value the value to which all coefficients are set
   *
   * Example: \include Matrix_setConstant_int_int.cpp
   * Output: \verbinclude Matrix_setConstant_int_int.out

Eigen/src/Core/DenseBase.h

@@ -45,14 +45,13 @@ template<typename Derived> class DenseBase
 #endif // not EIGEN_PARSED_BY_DOXYGEN
 {
   public:
-#ifndef EIGEN_PARSED_BY_DOXYGEN
     using ei_special_scalar_op_base<Derived,typename ei_traits<Derived>::Scalar,
                 typename NumTraits<typename ei_traits<Derived>::Scalar>::Real>::operator*;
 
     class InnerIterator;
 
     typedef typename ei_traits<Derived>::StorageKind StorageKind;
-    typedef typename ei_traits<Derived>::Index Index;
+    typedef typename ei_traits<Derived>::Index Index; /**< The type of indices */
     typedef typename ei_traits<Derived>::Scalar Scalar;
     typedef typename ei_packet_traits<Scalar>::type PacketScalar;
     typedef typename NumTraits<Scalar>::Real RealScalar;
@@ -90,8 +89,6 @@ template<typename Derived> class DenseBase
     using Base::colStride;
     using typename Base::CoeffReturnType;
 
-#endif // not EIGEN_PARSED_BY_DOXYGEN
-
     enum {
 
       RowsAtCompileTime = ei_traits<Derived>::RowsAtCompileTime,

Eigen/src/Core/SelfAdjointView.h

@@ -65,7 +65,10 @@ template<typename MatrixType, unsigned int UpLo> class SelfAdjointView
   public:
 
     typedef TriangularBase<SelfAdjointView> Base;
-    typedef typename ei_traits<SelfAdjointView>::Scalar Scalar;
+
+    /** \brief The type of coefficients in this matrix */
+    typedef typename ei_traits<SelfAdjointView>::Scalar Scalar; 
+
     typedef typename MatrixType::Index Index;
 
     enum {

Eigen/src/Geometry/Homogeneous.h

@@ -135,7 +135,7 @@ template<typename MatrixType,int _Direction> class Homogeneous
   *
   * \return an expression of the equivalent homogeneous vector
   *
-  * \vectoronly
+  * \only_for_vectors
   *
   * Example: \include MatrixBase_homogeneous.cpp
   * Output: \verbinclude MatrixBase_homogeneous.out

Eigen/src/Geometry/Quaternion.h

@@ -277,19 +277,6 @@ typedef Quaternion<double> Quaterniond;
 * Specialization of Map<Quaternion<Scalar>>
 ***************************************************************************/
 
-/** \class Map<Quaternion>
-  *
-  *
-  * \brief Expression of a quaternion from a memory buffer
-  *
-  * \param _Scalar the type of the Quaternion coefficients
-  * \param PacketAccess see class Map
-  *
-  * This is a specialization of class Map for Quaternion. This class allows to view
-  * a 4 scalar memory buffer as an Eigen's  Quaternion object.
-  *
-  * \sa class Map, class Quaternion, class QuaternionBase
-  */
 template<typename _Scalar, int _PacketAccess>
 struct ei_traits<Map<Quaternion<_Scalar>, _PacketAccess> >:
 ei_traits<Quaternion<_Scalar> >
@@ -301,6 +288,16 @@ ei_traits<Quaternion<_Scalar> >
   };
 };
 
+/** \brief Expression of a quaternion from a memory buffer
+  *
+  * \param _Scalar the type of the Quaternion coefficients
+  * \param PacketAccess see class Map
+  *
+  * This is a specialization of class Map for Quaternion. This class allows to view
+  * a 4 scalar memory buffer as an Eigen's  Quaternion object.
+  *
+  * \sa class Map, class Quaternion, class QuaternionBase
+  */
 template<typename _Scalar, int PacketAccess>
 class Map<Quaternion<_Scalar>, PacketAccess >
   : public QuaternionBase<Map<Quaternion<_Scalar>, PacketAccess> >

Eigen/src/Geometry/Transform.h

@@ -914,7 +914,7 @@ struct ei_projective_transform_inverse<TransformType, Projective>
   * \returns the inverse transformation according to some given knowledge
   * on \c *this.
   *
-  * \param traits allows to optimize the inversion process when the transformation
+  * \param hint allows to optimize the inversion process when the transformation
   * is known to be not a general transformation. The possible values are:
   *  - Projective if the transformation is not necessarily affine, i.e., if the
   *    last row is not guaranteed to be [0 ... 0 1]