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]

doc/C05_TutorialAdvancedInitialization.dox

@@ -87,7 +87,7 @@ Output: \verbinclude Tutorial_AdvancedInitialization_LinSpaced.out
 
 This example shows that objects like the ones returned by LinSpaced() can be assigned to variables (and
 expressions). Eigen defines utility functions like \link DenseBase::setZero() setZero()\endlink, 
-\link MatrixBase::setIdentity() \endlink and \link DenseBase:setLinSpaced() \endlink to do this
+\link MatrixBase::setIdentity() \endlink and \link DenseBase::setLinSpaced() \endlink to do this
 conveniently. The following example contrasts three ways to construct the matrix
 \f$ J = \bigl[ \begin{smallmatrix} O & I \\ I & O \end{smallmatrix} \bigr] \f$: using static methods and
 assignment, using static methods and the comma-initializer, or using the setXxx() methods.

doc/C07_TutorialReductionsVisitorsBroadcasting.dox

@@ -37,7 +37,7 @@ The \em trace of a matrix, as returned by the function \c trace(), is the sum of
 
 
 \subsection TutorialReductionsVisitorsBroadcastingReductionsNorm Norm reductions
-Eigen also provides reductions to obtain the Euclidean norm or squared norm of a vector with \link MatrixBase::norm() norm() \endlink and \link Matrix::squaredNorm() squaredNorm() \endlink respectively.
+Eigen also provides reductions to obtain the Euclidean norm or squared norm of a vector with \link MatrixBase::norm() norm() \endlink and \link MatrixBase::squaredNorm() squaredNorm() \endlink respectively.
 These operations can also operate on matrices; in that case, they use the Frobenius norm. The following example shows these methods. 
 
 <table class="tutorial_code"><tr><td>
@@ -190,7 +190,7 @@ reductions and partial reductions.
 
 Now that broadcasting, reductions and partial reductions have been introduced, we can dive into a more advanced example that finds
 the nearest neighbour of a vector <tt>v</tt> within the columns of matrix <tt>m</tt>. The Euclidean distance will be used in this example,
-computing the squared Euclidean distance with the partial reduction named \link DenseBase::squaredNorm() squaredNorm() \endlink:
+computing the squared Euclidean distance with the partial reduction named \link MatrixBase::squaredNorm() squaredNorm() \endlink:
 
 <table class="tutorial_code"><tr><td>
 Example: \include Tutorial_ReductionsVisitorsBroadcasting_broadcast_1nn.cpp

doc/QuickReference.dox

@@ -457,7 +457,7 @@ mat = 2 7 8
 \endcode</td></tr>
 </table>
 
-Special versions of \link DenseBase::minCoeff(int*,int*) minCoeff \endlink and \link DenseBase::maxCoeff(int*,int*) maxCoeff \endlink:
+Special versions of \link DenseBase::minCoeff(Index*,Index*) minCoeff \endlink and \link DenseBase::maxCoeff(Index*,Index*) maxCoeff \endlink:
 <div class="desired_tutorial_width">
 \code
 int i, j;
@@ -476,8 +476,8 @@ if((array1 < array2).any()) ... // if there exist a pair i,j such that array1(i,
 
 <a href="#" class="top">top</a>\section QuickRef_Blocks Sub-matrices
 
-Read-write access to a \link DenseBase::col(int) column \endlink
-or a \link DenseBase::row(int) row \endlink of a matrix (or array):
+Read-write access to a \link DenseBase::col(Index) column \endlink
+or a \link DenseBase::row(Index) row \endlink of a matrix (or array):
 <div class="desired_tutorial_width">
 \code
 mat1.row(i) = mat2.col(j);
@@ -501,9 +501,9 @@ Read-write access to sub-vectors:
 Read-write access to sub-matrices:</td><td></td><td></td></tr>
 <tr>
   <td>\code mat1.block(i,j,rows,cols)\endcode
-      \link DenseBase::block(int,int,int,int) (more) \endlink</td>
+      \link DenseBase::block(Index,Index,Index,Index) (more) \endlink</td>
   <td>\code mat1.block<rows,cols>(i,j)\endcode
-      \link DenseBase::block(int,int) (more) \endlink</td>
+      \link DenseBase::block(Index,Index) (more) \endlink</td>
   <td>the \c rows x \c cols sub-matrix \n starting from position (\c i,\c j)</td></tr>
 <tr><td>\code
  mat1.topLeftCorner(rows,cols)
@@ -547,7 +547,7 @@ Declare a diagonal matrix</td><td>\code
 DiagonalMatrix<Scalar,SizeAtCompileTime> diag1(size);
 diag1.diagonal() = vector;\endcode
 </td></tr>
-<tr><td>Access the \link MatrixBase::diagonal() diagonal \endlink and \link MatrixBase::diagonal(int) super/sub diagonals \endlink of a matrix as a vector (read/write)</td>
+<tr><td>Access the \link MatrixBase::diagonal() diagonal \endlink and \link MatrixBase::diagonal(Index) super/sub diagonals \endlink of a matrix as a vector (read/write)</td>
  <td>\code
 vec1 = mat1.diagonal();        mat1.diagonal() = vec1;      // main diagonal
 vec1 = mat1.diagonal(+n);      mat1.diagonal(+n) = vec1;    // n-th super diagonal