69 files changed, 2168 insertions, 1636 deletions

diff --git a/doc/A05_PortingFrom2To3.dox b/doc/A05_PortingFrom2To3.dox
index 10ce96870..4d5f3ae1f 100644
--- a/doc/A05_PortingFrom2To3.dox
+++ b/doc/A05_PortingFrom2To3.dox
@@ -2,31 +2,16 @@ namespace Eigen {
 
 /** \page Eigen2ToEigen3 Porting from Eigen2 to Eigen3
 
+<div class="bigwarning">Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3.</div>
+
 This page lists the most important API changes between Eigen2 and Eigen3,
 and gives tips to help porting your application from Eigen2 to Eigen3.
 
-\b Table \b of \b contents
-  - \ref CompatibilitySupport
-  - \ref Using
-  - \ref ComplexDot
-  - \ref VectorBlocks
-  - \ref Corners
-  - \ref CoefficientWiseOperations
-  - \ref PartAndExtract
-  - \ref TriangularSolveInPlace
-  - \ref Decompositions
-  - \ref LinearSolvers
-  - \ref GeometryModule
-  - \ref Transform
-  - \ref LazyVsNoalias
-  - \ref AlignMacros
-  - \ref AlignedMap
-  - \ref StdContainers
-  - \ref eiPrefix
+\eigenAutoToc
 
 \section CompatibilitySupport Eigen2 compatibility support
 
-In order to ease the switch from Eigen2 to Eigen3, Eigen3 features \ref Eigen2SupportModes "Eigen2 support modes".
+In order to ease the switch from Eigen2 to Eigen3, Eigen3 features \subpage Eigen2SupportModes "Eigen2 support modes".
 
 The quick way to enable this is to define the \c EIGEN2_SUPPORT preprocessor token \b before including any Eigen header (typically it should be set in your project options).
 
@@ -298,7 +283,7 @@ result = Vector4f::MapAligned(some_aligned_array);
 
 \section StdContainers STL Containers
 
-In Eigen2, #include<Eigen/StdVector> tweaked std::vector to automatically align elements. The problem was that that was quite invasive. In Eigen3, we only override standard behavior if you use Eigen::aligned_allocator<T> as your allocator type. So for example, if you use std::vector<Matrix4f>, you need to do the following change (note that aligned_allocator is under namespace Eigen):
+In Eigen2, <tt>#include<Eigen/StdVector></tt> tweaked std::vector to automatically align elements. The problem was that that was quite invasive. In Eigen3, we only override standard behavior if you use Eigen::aligned_allocator<T> as your allocator type. So for example, if you use std::vector<Matrix4f>, you need to do the following change (note that aligned_allocator is under namespace Eigen):
 
 <table class="manual">
 <tr><th>Eigen 2</th><th>Eigen 3</th></tr>
diff --git a/doc/A10_Eigen2SupportModes.dox b/doc/A10_Eigen2SupportModes.dox
index c20b64eed..f3df91515 100644
--- a/doc/A10_Eigen2SupportModes.dox
+++ b/doc/A10_Eigen2SupportModes.dox
@@ -2,18 +2,12 @@ namespace Eigen {
 
 /** \page Eigen2SupportModes Eigen 2 support modes
 
+<div class="bigwarning">Eigen2 support is deprecated in Eigen 3.2.x and it will be removed in Eigen 3.3.</div>
+
 This page documents the Eigen2 support modes, a powerful tool to help migrating your project from Eigen 2 to Eigen 3.
 Don't miss our page on \ref Eigen2ToEigen3 "API changes" between Eigen 2 and Eigen 3.
 
-\b Table \b of \b contents
-  - \ref EIGEN2_SUPPORT_Macro
-  - \ref StagedMigrationPathOverview
-  - \ref Stage10
-  - \ref Stage20
-  - \ref Stage30
-  - \ref Stage40
-  - \ref FinallyDropAllEigen2Support
-  - \ref ABICompatibility
+\eigenAutoToc
 
 \section EIGEN2_SUPPORT_Macro The quick way: define EIGEN2_SUPPORT
 
diff --git a/doc/AsciiQuickReference.txt b/doc/AsciiQuickReference.txt
index d2e973f5d..1e74e0528 100644
--- a/doc/AsciiQuickReference.txt
+++ b/doc/AsciiQuickReference.txt
@@ -1,8 +1,7 @@
 // A simple quickref for Eigen. Add anything that's missing.
 // Main author: Keir Mierle
 
-#include <Eigen/Core>
-#include <Eigen/Array>
+#include <Eigen/Dense>
 
 Matrix<double, 3, 3> A;               // Fixed rows and cols. Same as Matrix3d.
 Matrix<double, 3, Dynamic> B;         // Fixed rows, dynamic cols.
@@ -11,13 +10,14 @@ Matrix<double, 3, 3, RowMajor> E;     // Row major; default is column-major.
 Matrix3f P, Q, R;                     // 3x3 float matrix.
 Vector3f x, y, z;                     // 3x1 float matrix.
 RowVector3f a, b, c;                  // 1x3 float matrix.
+VectorXd v;                           // Dynamic column vector of doubles
 double s;                            
 
 // Basic usage
 // Eigen          // Matlab           // comments
 x.size()          // length(x)        // vector size
-C.rows()          // size(C)(1)       // number of rows
-C.cols()          // size(C)(2)       // number of columns
+C.rows()          // size(C,1)        // number of rows
+C.cols()          // size(C,2)        // number of columns
 x(i)              // x(i+1)           // Matlab is 1-based
 C(i,j)            // C(i+1,j+1)       //
 
@@ -31,9 +31,19 @@ A << 1, 2, 3,     // Initialize A. The elements can also be
      7, 8, 9;     // and then the rows are stacked.
 B << A, A, A;     // B is three horizontally stacked A's.
 A.fill(10);       // Fill A with all 10's.
-A.setRandom();    // Fill A with uniform random numbers in (-1, 1).
-                  // Requires #include <Eigen/Array>.
-A.setIdentity();  // Fill A with the identity.
+
+// Eigen                            // Matlab
+MatrixXd::Identity(rows,cols)       // eye(rows,cols)
+C.setIdentity(rows,cols)            // C = eye(rows,cols)
+MatrixXd::Zero(rows,cols)           // zeros(rows,cols)
+C.setZero(rows,cols)                // C = ones(rows,cols)
+MatrixXd::Ones(rows,cols)           // ones(rows,cols)
+C.setOnes(rows,cols)                // C = ones(rows,cols)
+MatrixXd::Random(rows,cols)         // rand(rows,cols)*2-1        // MatrixXd::Random returns uniform random numbers in (-1, 1).
+C.setRandom(rows,cols)              // C = rand(rows,cols)*2-1
+VectorXd::LinSpaced(size,low,high)   // linspace(low,high,size)'
+v.setLinSpaced(size,low,high)        // v = linspace(low,high,size)'
+
 
 // Matrix slicing and blocks. All expressions listed here are read/write.
 // Templated size versions are faster. Note that Matlab is 1-based (a size N
@@ -41,20 +51,34 @@ A.setIdentity();  // Fill A with the identity.
 // Eigen                           // Matlab
 x.head(n)                          // x(1:n)
 x.head<n>()                        // x(1:n)
-x.tail(n)                          // N = rows(x); x(N - n: N)
-x.tail<n>()                        // N = rows(x); x(N - n: N)
+x.tail(n)                          // x(end - n + 1: end)
+x.tail<n>()                        // x(end - n + 1: end)
 x.segment(i, n)                    // x(i+1 : i+n)
 x.segment<n>(i)                    // x(i+1 : i+n)
 P.block(i, j, rows, cols)          // P(i+1 : i+rows, j+1 : j+cols)
 P.block<rows, cols>(i, j)          // P(i+1 : i+rows, j+1 : j+cols)
+P.row(i)                           // P(i+1, :)
+P.col(j)                           // P(:, j+1)
+P.leftCols<cols>()                 // P(:, 1:cols)
+P.leftCols(cols)                   // P(:, 1:cols)
+P.middleCols<cols>(j)              // P(:, j+1:j+cols)
+P.middleCols(j, cols)              // P(:, j+1:j+cols)
+P.rightCols<cols>()                // P(:, end-cols+1:end)
+P.rightCols(cols)                  // P(:, end-cols+1:end)
+P.topRows<rows>()                  // P(1:rows, :)
+P.topRows(rows)                    // P(1:rows, :)
+P.middleRows<rows>(i)              // P(:, i+1:i+rows)
+P.middleRows(i, rows)              // P(:, i+1:i+rows)
+P.bottomRows<rows>()               // P(:, end-rows+1:end)
+P.bottomRows(rows)                 // P(:, end-rows+1:end)
 P.topLeftCorner(rows, cols)        // P(1:rows, 1:cols)
-P.topRightCorner(rows, cols)       // [m n]=size(P); P(1:rows, n-cols+1:n)
-P.bottomLeftCorner(rows, cols)     // [m n]=size(P); P(m-rows+1:m, 1:cols)
-P.bottomRightCorner(rows, cols)    // [m n]=size(P); P(m-rows+1:m, n-cols+1:n)
+P.topRightCorner(rows, cols)       // P(1:rows, end-cols+1:end)
+P.bottomLeftCorner(rows, cols)     // P(end-rows+1:end, 1:cols)
+P.bottomRightCorner(rows, cols)    // P(end-rows+1:end, end-cols+1:end)
 P.topLeftCorner<rows,cols>()       // P(1:rows, 1:cols)
-P.topRightCorner<rows,cols>()      // [m n]=size(P); P(1:rows, n-cols+1:n)
-P.bottomLeftCorner<rows,cols>()    // [m n]=size(P); P(m-rows+1:m, 1:cols)
-P.bottomRightCorner<rows,cols>()   // [m n]=size(P); P(m-rows+1:m, n-cols+1:n)
+P.topRightCorner<rows,cols>()      // P(1:rows, end-cols+1:end)
+P.bottomLeftCorner<rows,cols>()    // P(end-rows+1:end, 1:cols)
+P.bottomRightCorner<rows,cols>()   // P(end-rows+1:end, end-cols+1:end)
 
 // Of particular note is Eigen's swap function which is highly optimized.
 // Eigen                           // Matlab
@@ -67,6 +91,8 @@ R.adjoint()                        // R'
 R.transpose()                      // R.' or conj(R')
 R.diagonal()                       // diag(R)
 x.asDiagonal()                     // diag(x)
+R.transpose().colwise().reverse(); // rot90(R)
+R.conjugate()                      // conj(R)
 
 // All the same as Matlab, but matlab doesn't have *= style operators.
 // Matrix-vector.  Matrix-matrix.   Matrix-scalar.
@@ -77,8 +103,7 @@ a *= M;            R  = P + Q;      R  = P/s;
                    R += Q;          R *= s;
                    R -= Q;          R /= s;
 
- // Vectorized operations on each element independently
- // (most require #include <Eigen/Array>)
+// Vectorized operations on each element independently
 // Eigen                  // Matlab
 R = P.cwiseProduct(Q);    // R = P .* Q
 R = P.array() * s.array();// R = P .* s
@@ -116,16 +141,14 @@ int r, c;
 // Eigen                  // Matlab
 R.minCoeff()              // min(R(:))
 R.maxCoeff()              // max(R(:))
-s = R.minCoeff(&r, &c)    // [aa, bb] = min(R); [cc, dd] = min(aa);
-                          // r = bb(dd); c = dd; s = cc
-s = R.maxCoeff(&r, &c)    // [aa, bb] = max(R); [cc, dd] = max(aa);
-                          // row = bb(dd); col = dd; s = cc
+s = R.minCoeff(&r, &c)    // [s, i] = min(R(:)); [r, c] = ind2sub(size(R), i);
+s = R.maxCoeff(&r, &c)    // [s, i] = max(R(:)); [r, c] = ind2sub(size(R), i);
 R.sum()                   // sum(R(:))
-R.colwise.sum()           // sum(R)
-R.rowwise.sum()           // sum(R, 2) or sum(R')'
+R.colwise().sum()         // sum(R)
+R.rowwise().sum()         // sum(R, 2) or sum(R')'
 R.prod()                  // prod(R(:))
-R.colwise.prod()          // prod(R)
-R.rowwise.prod()          // prod(R, 2) or prod(R')'
+R.colwise().prod()        // prod(R)
+R.rowwise().prod()        // prod(R, 2) or prod(R')'
 R.trace()                 // trace(R)
 R.all()                   // all(R(:))
 R.colwise().all()         // all(R)
@@ -141,21 +164,34 @@ x.squaredNorm()           // dot(x, x)   Note the equivalence is not true for co
 x.dot(y)                  // dot(x, y)
 x.cross(y)                // cross(x, y) Requires #include <Eigen/Geometry>
 
+//// Type conversion
+// Eigen                           // Matlab
+A.cast<double>();                  // double(A)
+A.cast<float>();                   // single(A)
+A.cast<int>();                     // int32(A)
+A.real();                          // real(A)
+A.imag();                          // imag(A)
+// if the original type equals destination type, no work is done
+
+// Note that for most operations Eigen requires all operands to have the same type:
+MatrixXf F = MatrixXf::Zero(3,3);
+A += F;                // illegal in Eigen. In Matlab A = A+F is allowed
+A += F.cast<double>(); // F converted to double and then added (generally, conversion happens on-the-fly)
+
 // Eigen can map existing memory into Eigen matrices.
 float array[3];
-Map<Vector3f>(array, 3).fill(10);
-int data[4] = 1, 2, 3, 4;
-Matrix2i mat2x2(data);
-MatrixXi mat2x2 = Map<Matrix2i>(data);
-MatrixXi mat2x2 = Map<MatrixXi>(data, 2, 2);
+Vector3f::Map(array).fill(10);            // create a temporary Map over array and sets entries to 10
+int data[4] = {1, 2, 3, 4};
+Matrix2i mat2x2(data);                    // copies data into mat2x2
+Matrix2i::Map(data) = 2*mat2x2;           // overwrite elements of data with 2*mat2x2
+MatrixXi::Map(data, 2, 2) += mat2x2;      // adds mat2x2 to elements of data (alternative syntax if size is not know at compile time)
 
 // Solve Ax = b. Result stored in x. Matlab: x = A \ b.
-bool solved;
-solved = A.ldlt().solve(b, &x));  // A sym. p.s.d.    #include <Eigen/Cholesky>
-solved = A.llt() .solve(b, &x));  // A sym. p.d.      #include <Eigen/Cholesky>
-solved = A.lu()  .solve(b, &x));  // Stable and fast. #include <Eigen/LU>
-solved = A.qr()  .solve(b, &x));  // No pivoting.     #include <Eigen/QR>
-solved = A.svd() .solve(b, &x));  // Stable, slowest. #include <Eigen/SVD>
+x = A.ldlt().solve(b));  // A sym. p.s.d.    #include <Eigen/Cholesky>
+x = A.llt() .solve(b));  // A sym. p.d.      #include <Eigen/Cholesky>
+x = A.lu()  .solve(b));  // Stable and fast. #include <Eigen/LU>
+x = A.qr()  .solve(b));  // No pivoting.     #include <Eigen/QR>
+x = A.svd() .solve(b));  // Stable, slowest. #include <Eigen/SVD>
 // .ldlt() -> .matrixL() and .matrixD()
 // .llt()  -> .matrixL()
 // .lu()   -> .matrixL() and .matrixU()
@@ -168,3 +204,4 @@ A.eigenvalues();                  // eig(A);
 EigenSolver<Matrix3d> eig(A);     // [vec val] = eig(A)
 eig.eigenvalues();                // diag(val)
 eig.eigenvectors();               // vec
+// For self-adjoint matrices use SelfAdjointEigenSolver<>
diff --git a/doc/B01_Experimental.dox b/doc/B01_Experimental.dox
index 6d8b90d5a..5fc0ccd60 100644
--- a/doc/B01_Experimental.dox
+++ b/doc/B01_Experimental.dox
@@ -2,10 +2,7 @@ namespace Eigen {
 
 /** \page Experimental Experimental parts of Eigen
 
-\b Table \b of \b contents
-  - \ref summary
-  - \ref modules
-  - \ref core
+\eigenAutoToc
 
 \section summary Summary
 
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index 96bff41bf..8a493031c 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -10,14 +10,28 @@ if(CMAKE_COMPILER_IS_GNUCXX)
   endif(CMAKE_SYSTEM_NAME MATCHES Linux)
 endif(CMAKE_COMPILER_IS_GNUCXX)
 
+# Set some Doxygen flags
+set(EIGEN_DOXY_PROJECT_NAME             "Eigen")
+set(EIGEN_DOXY_OUTPUT_DIRECTORY_SUFFIX  "")
+set(EIGEN_DOXY_INPUT                    "\"${Eigen_SOURCE_DIR}/Eigen\" \"${Eigen_SOURCE_DIR}/doc\"")
+set(EIGEN_DOXY_HTML_COLORSTYLE_HUE      "220")
+set(EIGEN_DOXY_TAGFILES                 "")
+
 configure_file(
-  ${Eigen_SOURCE_DIR}/unsupported/doc/Doxyfile.in
-  ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile-unsupported
+  ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
+  ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
 )
 
+set(EIGEN_DOXY_PROJECT_NAME             "Eigen-unsupported")
+set(EIGEN_DOXY_OUTPUT_DIRECTORY_SUFFIX  "/unsupported")
+set(EIGEN_DOXY_INPUT                    "\"${Eigen_SOURCE_DIR}/unsupported/Eigen\" \"${Eigen_SOURCE_DIR}/unsupported/doc\"")
+set(EIGEN_DOXY_HTML_COLORSTYLE_HUE      "0")
+# set(EIGEN_DOXY_TAGFILES                 "\"${Eigen_BINARY_DIR}/doc/eigen.doxytags =../\"")
+set(EIGEN_DOXY_TAGFILES                 "")
+
 configure_file(
   ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in
-  ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+  ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile-unsupported
 )
 
 configure_file(
@@ -30,10 +44,21 @@ configure_file(
   ${CMAKE_CURRENT_BINARY_DIR}/eigendoxy_footer.html
 )
 
+configure_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/eigendoxy_layout.xml.in
+  ${CMAKE_CURRENT_BINARY_DIR}/eigendoxy_layout.xml
+)
+
+configure_file(
+  ${Eigen_SOURCE_DIR}/unsupported/doc/eigendoxy_layout.xml.in
+  ${Eigen_BINARY_DIR}/doc/unsupported/eigendoxy_layout.xml
+)
+
 set(examples_targets "")
 set(snippets_targets "")
 
 add_definitions("-DEIGEN_MAKING_DOCS")
+add_custom_target(all_examples)
 
 add_subdirectory(examples)
 add_subdirectory(special_examples)
@@ -43,12 +68,9 @@ add_custom_target(
   doc-eigen-prerequisites
   ALL
   COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_CURRENT_BINARY_DIR}/html/
-  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/eigendoxy_tabs.css
-                                   ${CMAKE_CURRENT_BINARY_DIR}/html/
-  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/Eigen_Silly_Professor_64x64.png
-                                   ${CMAKE_CURRENT_BINARY_DIR}/html/
-  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/AsciiQuickReference.txt
-                                   ${CMAKE_CURRENT_BINARY_DIR}/html/
+  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/eigen_navtree_hacks.js           ${CMAKE_CURRENT_BINARY_DIR}/html/
+  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/Eigen_Silly_Professor_64x64.png  ${CMAKE_CURRENT_BINARY_DIR}/html/
+  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/AsciiQuickReference.txt          ${CMAKE_CURRENT_BINARY_DIR}/html/
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 )
 
@@ -56,10 +78,8 @@ add_custom_target(
   doc-unsupported-prerequisites
   ALL
   COMMAND ${CMAKE_COMMAND} -E make_directory ${Eigen_BINARY_DIR}/doc/html/unsupported
-  COMMAND ${CMAKE_COMMAND} -E copy ${Eigen_SOURCE_DIR}/doc/eigendoxy_tabs.css
-                                   ${Eigen_BINARY_DIR}/doc/html/unsupported/
-  COMMAND ${CMAKE_COMMAND} -E copy ${Eigen_SOURCE_DIR}/doc/Eigen_Silly_Professor_64x64.png
-                                   ${Eigen_BINARY_DIR}/doc/html/unsupported/
+  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/eigen_navtree_hacks.js           ${CMAKE_CURRENT_BINARY_DIR}/html/unsupported/
+  COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/Eigen_Silly_Professor_64x64.png  ${CMAKE_CURRENT_BINARY_DIR}/html/unsupported/
   WORKING_DIRECTORY ${Eigen_BINARY_DIR}/doc
 )
 
@@ -67,11 +87,11 @@ add_dependencies(doc-eigen-prerequisites all_snippets all_examples)
 add_dependencies(doc-unsupported-prerequisites unsupported_snippets unsupported_examples)
 
 add_custom_target(doc ALL
-  COMMAND doxygen Doxyfile-unsupported
   COMMAND doxygen
-  COMMAND doxygen Doxyfile-unsupported # run doxygen twice to get proper eigen <=> unsupported cross references
+  COMMAND doxygen Doxyfile-unsupported
   COMMAND ${CMAKE_COMMAND} -E rename html eigen-doc
-  COMMAND ${CMAKE_COMMAND} -E tar cvfz eigen-doc/eigen-doc.tgz eigen-doc/*.html eigen-doc/*.map eigen-doc/*.png eigen-doc/*.css eigen-doc/*.js eigen-doc/*.txt eigen-doc/unsupported
+  COMMAND ${CMAKE_COMMAND} -E remove eigen-doc/eigen-doc.tgz
+  COMMAND ${CMAKE_COMMAND} -E tar cfz eigen-doc/eigen-doc.tgz eigen-doc
   COMMAND ${CMAKE_COMMAND} -E rename eigen-doc html
   WORKING_DIRECTORY ${Eigen_BINARY_DIR}/doc)
 
diff --git a/doc/I12_ClassHierarchy.dox b/doc/ClassHierarchy.dox
index 700d01802..468e60a76 100644
--- a/doc/I12_ClassHierarchy.dox
+++ b/doc/ClassHierarchy.dox
@@ -6,11 +6,7 @@ This page explains the design of the core classes in Eigen's class hierarchy and
 users probably need not concern themselves with these details, but it may be useful for both advanced users
 and Eigen developers.
 
-<b>Table of contents</b>
-  - \ref TopicClassHierarchyPrinciples
-  - \ref TopicClassHierarchyCoreClasses
-  - \ref TopicClassHierarchyBaseClasses
-  - \ref TopicClassHierarchyInheritanceDiagrams 
+\eigenAutoToc
 
 
 \section TopicClassHierarchyPrinciples Principles
diff --git a/doc/I00_CustomizingEigen.dox b/doc/CustomizingEigen.dox
index aa4514d68..5a0890ea9 100644
--- a/doc/I00_CustomizingEigen.dox
+++ b/doc/CustomizingEigen.dox
@@ -4,10 +4,7 @@ namespace Eigen {
 
 Eigen can be extended in several ways, for instance, by defining global methods, \ref ExtendingMatrixBase "by adding custom methods to MatrixBase", adding support to \ref CustomScalarType "custom types" etc.
 
-\b Table \b of \b contents
-  - \ref ExtendingMatrixBase
-  - \ref InheritingFromMatrix
-  - \ref CustomScalarType
+\eigenAutoToc
 
 \section ExtendingMatrixBase Extending MatrixBase (and other classes)
 
@@ -127,7 +124,7 @@ Eigen::MatrixBase<Eigen::Matrix<std::complex<float>, 10000, 1, 2, 10000, 1>
 
 \anchor user_defined_scalars \section CustomScalarType Using custom scalar types
 
-By default, Eigen currently supports standard floating-point types (\c float, \c double, \c std::complex<float>, \c std::complex<double>, \c long \c double), as well as all integrale types (e.g., \c int, \c unsigned \c int, \c short, etc.), and \c bool.
+By default, Eigen currently supports standard floating-point types (\c float, \c double, \c std::complex<float>, \c std::complex<double>, \c long \c double), as well as all native integer types (e.g., \c int, \c unsigned \c int, \c short, etc.), and \c bool.
 On x86-64 systems, \c long \c double permits to locally enforces the use of x87 registers with extended accuracy (in comparison to SSE).
 
 In order to add support for a custom type \c T you need:
@@ -136,7 +133,7 @@ In order to add support for a custom type \c T you need:
 -# define the math functions that makes sense for your type. This includes standard ones like sqrt, pow, sin, tan, conj, real, imag, etc, as well as abs2 which is Eigen specific.
      (see the file Eigen/src/Core/MathFunctions.h)
 
-The math function should be defined in the same namespace than \c T, or in the \c std namespace though that second appraoch is not recommended.
+The math function should be defined in the same namespace than \c T, or in the \c std namespace though that second approach is not recommended.
 
 Here is a concrete example adding support for the Adolc's \c adouble type. <a href="https://projects.coin-or.org/ADOL-C">Adolc</a> is an automatic differentiation library. The type \c adouble is basically a real value tracking the values of any number of partial derivatives.
 
diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
index e9e89d486..1a2603b04 100644
--- a/doc/Doxyfile.in
+++ b/doc/Doxyfile.in
@@ -1,12 +1,14 @@
+# Doxyfile 1.8.1.1
+
 # This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
+# doxygen (www.doxygen.org) for a project.
 #
-# All text after a hash (#) is considered a comment and will be ignored
+# All text after a hash (#) is considered a comment and will be ignored.
 # The format is:
 #       TAG = value [value, ...]
 # For lists items can also be appended using:
 #       TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
+# Values that contain spaces should be placed between quotes (" ").
 
 #---------------------------------------------------------------------------
 # Project related configuration options
@@ -20,24 +22,39 @@
 
 DOXYFILE_ENCODING      = UTF-8
 
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
-# by quotes) that should identify the project.
+# The PROJECT_NAME tag is a single word (or sequence of words) that should
+# identify the project. Note that if you do not use Doxywizard you need
+# to put quotes around the project name if it contains spaces.
 
-PROJECT_NAME           = Eigen
+PROJECT_NAME           = ${EIGEN_DOXY_PROJECT_NAME}
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number.
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 
-#EIGEN_VERSION is set in the root CMakeLists.txt
+# EIGEN_VERSION is set in the root CMakeLists.txt
+
 PROJECT_NUMBER         = "${EIGEN_VERSION}"
 
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer
+# a quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF          =
+
+# With the PROJECT_LOGO tag one can specify an logo or icon that is
+# included in the documentation. The maximum height of the logo should not
+# exceed 55 pixels and the maximum width should not exceed 200 pixels.
+# Doxygen will copy the logo to the output directory.
+
+PROJECT_LOGO           = "${Eigen_SOURCE_DIR}/doc/Eigen_Silly_Professor_64x64.png"
+
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = "${Eigen_BINARY_DIR}/doc"
+OUTPUT_DIRECTORY       = "${Eigen_BINARY_DIR}/doc${EIGEN_DOXY_OUTPUT_DIRECTORY_SUFFIX}"
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -53,11 +70,11 @@ CREATE_SUBDIRS         = NO
 # information to generate all constant output in the proper language.
 # The default language is English, other supported languages are:
 # Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
-# Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek,
-# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages),
-# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish,
-# Portuguese, Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish,
-# and Ukrainian.
+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
 
 OUTPUT_LANGUAGE        = English
 
@@ -135,7 +152,7 @@ STRIP_FROM_PATH        =
 STRIP_FROM_INC_PATH    =
 
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful is your file systems
+# (but less readable) file names. This can be useful if your file system
 # doesn't support long names like on DOS, Mac, or CD-ROM.
 
 SHORT_NAMES            = NO
@@ -164,13 +181,6 @@ QT_AUTOBRIEF           = NO
 
 MULTILINE_CPP_IS_BRIEF = NO
 
-# If the DETAILS_AT_TOP tag is set to YES then Doxygen
-# will output the detailed description near the top, like JavaDoc.
-# If set to NO, the detailed description appears after the member
-# documentation.
-
-DETAILS_AT_TOP         = YES
-
 # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
 # member inherits the documentation from any documented member that it
 # re-implements.
@@ -211,7 +221,18 @@ ALIASES                = "only_for_vectors=This is only for vectors (either row-
                          "note_about_arbitrary_choice_of_solution=If there exists more than one solution, this method will arbitrarily choose one." \
                          "note_about_using_kernel_to_study_multiple_solutions=If you need a complete analysis of the space of solutions, take the one solution obtained by this method and add to it elements of the kernel, as determined by kernel()." \
                          "note_about_checking_solutions=This method just tries to find as good a solution as possible. If you want to check whether a solution exists or if it is accurate, just call this function to get a result and then compute the error of this result, or use MatrixBase::isApprox() directly, for instance like this: \code bool a_solution_exists = (A*result).isApprox(b, precision); \endcode This method avoids dividing by zero, so that the non-existence of a solution doesn't by itself mean that you'll get \c inf or \c nan values." \
-                         "note_try_to_help_rvo=This function returns the result by value. In order to make that efficient, it is implemented as just a return statement using a special constructor, hopefully allowing the compiler to perform a RVO (return value optimization)."
+                         "note_try_to_help_rvo=This function returns the result by value. In order to make that efficient, it is implemented as just a return statement using a special constructor, hopefully allowing the compiler to perform a RVO (return value optimization)." \
+                         "nonstableyet=\warning This is not considered to be part of the stable public API yet. Changes may happen in future releases. See \ref Experimental \"Experimental parts of Eigen\"
+
+ALIASES += "eigenAutoToc=  "
+ALIASES += "eigenManualPage=\defgroup"
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding
+# "class=itcl::class" will allow you to use the command class in the
+# itcl::class meaning.
+
+TCL_SUBST              =
 
 # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
 # sources only. Doxygen will then generate output that is more tailored for C.
@@ -239,11 +260,32 @@ OPTIMIZE_FOR_FORTRAN   = NO
 
 OPTIMIZE_OUTPUT_VHDL   = NO
 
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given extension.
+# Doxygen has a built-in mapping, but you can override or extend it using this
+# tag. The format is ext=language, where ext is a file extension, and language
+# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
+# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
+# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
+# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+
+EXTENSION_MAPPING      =
+
+# If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all
+# comments according to the Markdown format, which allows for more readable
+# documentation. See http://daringfireball.net/projects/markdown/ for details.
+# The output of markdown processing is further processed by doxygen, so you
+# can mix doxygen, HTML, and XML commands with Markdown formatting.
+# Disable only in case of backward compatibilities issues.
+
+MARKDOWN_SUPPORT       = YES
+
 # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
 # to include (a tag file for) the STL sources as input, then you should
 # set this tag to YES in order to let doxygen match functions declarations and
 # definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also make the inheritance and collaboration
+# func(std::string) {}). This also makes the inheritance and collaboration
 # diagrams that involve STL classes more complete and accurate.
 
 BUILTIN_STL_SUPPORT    = NO
@@ -261,7 +303,7 @@ SIP_SUPPORT            = NO
 
 # For Microsoft's IDL there are propget and propput attributes to indicate getter
 # and setter methods for a property. Setting this option to YES (the default)
-# will make doxygen to replace the get and set methods by a property in the
+# will make doxygen replace the get and set methods by a property in the
 # documentation. This will only work if the methods are indeed getting or
 # setting a simple type. If this is not the case, or you want to show the
 # methods anyway, you should set this option to NO.
@@ -283,6 +325,22 @@ DISTRIBUTE_GROUP_DOC   = NO
 
 SUBGROUPING            = YES
 
+# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
+# unions are shown inside the group in which they are included (e.g. using
+# @ingroup) instead of on a separate page (for HTML and Man pages) or
+# section (for LaTeX and RTF).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
+# unions with only public data fields will be shown inline in the documentation
+# of the scope in which they are defined (i.e. file, namespace, or group
+# documentation), provided this scope is documented. If set to NO (the default),
+# structs, classes, and unions are shown on a separate page (for HTML and Man
+# pages) or section (for LaTeX and RTF).
+
+INLINE_SIMPLE_STRUCTS  = NO
+
 # When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
 # is documented as struct, union, or enum with the name of the typedef. So
 # typedef struct TypeS {} TypeT, will appear in the documentation as a struct
@@ -293,6 +351,33 @@ SUBGROUPING            = YES
 
 TYPEDEF_HIDES_STRUCT   = NO
 
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penalty.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will roughly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+SYMBOL_CACHE_SIZE      = 0
+
+# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
+# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
+# their name and scope. Since this can be an expensive process and often the
+# same symbol appear multiple times in the code, doxygen keeps a cache of
+# pre-resolved symbols. If the cache is too small doxygen will become slower.
+# If the cache is too large, memory is wasted. The cache size is given by this
+# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+LOOKUP_CACHE_SIZE      = 0
+
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -302,13 +387,17 @@ TYPEDEF_HIDES_STRUCT   = NO
 # Private class members and static file members will be hidden unless
 # the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
 
-EXTRACT_ALL            = YES
+EXTRACT_ALL            = NO
 
 # If the EXTRACT_PRIVATE tag is set to YES all private members of a class
 # will be included in the documentation.
 
 EXTRACT_PRIVATE        = NO
 
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal scope will be included in the documentation.
+
+EXTRACT_PACKAGE        = NO
+
 # If the EXTRACT_STATIC tag is set to YES all static members of a file
 # will be included in the documentation.
 
@@ -331,7 +420,7 @@ EXTRACT_LOCAL_METHODS  = NO
 # extracted and appear in the documentation as a namespace called
 # 'anonymous_namespace{file}', where file will be replaced with the base
 # name of the file that contains the anonymous namespace. By default
-# anonymous namespace are hidden.
+# anonymous namespaces are hidden.
 
 EXTRACT_ANON_NSPACES   = NO
 
@@ -389,7 +478,13 @@ HIDE_SCOPE_NAMES       = YES
 # will put a list of the files that are included by a file in the documentation
 # of that file.
 
-SHOW_INCLUDE_FILES     = YES
+SHOW_INCLUDE_FILES     = NO
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
+# will list include files with double quotes in the documentation
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES   = NO
 
 # If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
 # is inserted in the documentation for inline members.
@@ -410,6 +505,16 @@ SORT_MEMBER_DOCS       = YES
 
 SORT_BRIEF_DOCS        = YES
 
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
+# will sort the (brief and detailed) documentation of class members so that
+# constructors and destructors are listed first. If set to NO (the default)
+# the constructors will appear in the respective orders defined by
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
 # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
 # hierarchy of group names into alphabetical order. If set to NO (the default)
 # the group names will appear in their defined order.
@@ -426,6 +531,15 @@ SORT_GROUP_NAMES       = NO
 
 SORT_BY_SCOPE_NAME     = NO
 
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# do proper type resolution of all parameters of a function it will reject a
+# match between the prototype and the implementation of a member function even
+# if there is only one candidate or it is obvious which candidate to choose
+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
+# will still accept a match between prototype and implementation in such cases.
+
+STRICT_PROTO_MATCHING  = NO
+
 # The GENERATE_TODOLIST tag can be used to enable (YES) or
 # disable (NO) the todo list. This list is created by putting \todo
 # commands in the documentation.
@@ -456,10 +570,10 @@ GENERATE_DEPRECATEDLIST= NO
 ENABLED_SECTIONS       =
 
 # The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or define consists of for it to appear in
+# the initial value of a variable or macro consists of for it to appear in
 # the documentation. If the initializer consists of more lines than specified
 # here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and defines in the
+# The appearance of the initializer of individual variables and macros in the
 # documentation can be controlled using \showinitializer or \hideinitializer
 # command in the documentation regardless of this setting.
 
@@ -471,12 +585,6 @@ MAX_INITIALIZER_LINES  = 0
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = NO
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
@@ -484,10 +592,11 @@ SHOW_DIRECTORIES       = NO
 SHOW_FILES             = YES
 
 # Set the SHOW_NAMESPACES tag to NO to disable the generation of the
-# Namespaces page.  This will remove the Namespaces entry from the Quick Index
+# Namespaces page.
+# This will remove the Namespaces entry from the Quick Index
 # and from the Folder Tree View (if specified). The default is YES.
 
-SHOW_NAMESPACES        = YES
+SHOW_NAMESPACES        = NO
 
 # The FILE_VERSION_FILTER tag can be used to specify a program or script that
 # doxygen should invoke to get the current version for each file (typically from
@@ -499,6 +608,25 @@ SHOW_NAMESPACES        = YES
 
 FILE_VERSION_FILTER    =
 
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. To create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option.
+# You can optionally specify a file name after the option, if omitted
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE            = "${Eigen_BINARY_DIR}/doc${EIGEN_DOXY_OUTPUT_DIRECTORY_SUFFIX}/eigendoxy_layout.xml"
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files
+# containing the references data. This must be a list of .bib files. The
+# .bib extension is automatically appended if omitted. Using this command
+# requires the bibtex tool to be installed. See also
+# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
+# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
+# feature you need bibtex and perl available in the search path.
+
+CITE_BIB_FILES         =
+
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
@@ -527,7 +655,7 @@ WARN_IF_UNDOCUMENTED   = NO
 
 WARN_IF_DOC_ERROR      = YES
 
-# This WARN_NO_PARAMDOC option can be abled to get warnings for
+# The WARN_NO_PARAMDOC option can be enabled to get warnings for
 # functions that are documented, but have no documentation for their parameters
 # or return value. If set to NO (the default) doxygen will only warn about
 # wrong or incomplete parameter documentation, but not about the absence of
@@ -559,8 +687,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = "${Eigen_SOURCE_DIR}/Eigen" \
-                         "${Eigen_SOURCE_DIR}/doc"
+INPUT                  = ${EIGEN_DOXY_INPUT}
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -574,8 +701,9 @@ INPUT_ENCODING         = UTF-8
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
 # and *.h) to filter out the source-files in the directories. If left
 # blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
+# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
+# *.f90 *.f *.for *.vhd *.vhdl
 
 FILE_PATTERNS          = *
 
@@ -585,18 +713,22 @@ FILE_PATTERNS          = *
 
 RECURSIVE              = YES
 
-# The EXCLUDE tag can be used to specify files and/or directories that should
+# The EXCLUDE tag can be used to specify files and/or directories that should be
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
 
 EXCLUDE                = "${Eigen_SOURCE_DIR}/Eigen/Eigen2Support" \
                          "${Eigen_SOURCE_DIR}/Eigen/src/Eigen2Support" \
                          "${Eigen_SOURCE_DIR}/doc/examples" \
                          "${Eigen_SOURCE_DIR}/doc/special_examples" \
-                         "${Eigen_SOURCE_DIR}/doc/snippets" 
+                         "${Eigen_SOURCE_DIR}/doc/snippets" \
+                         "${Eigen_SOURCE_DIR}/unsupported/doc/examples" \
+                         "${Eigen_SOURCE_DIR}/unsupported/doc/snippets"
 
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
-# directories that are symbolic links (a Unix filesystem feature) are excluded
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system feature) are excluded
 # from the input.
 
 EXCLUDE_SYMLINKS       = NO
@@ -607,21 +739,21 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories
 # for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =  CMake* \
-                          *.txt \
-                          *.sh \
-                          *.orig \
-                          *.diff \
-                          diff \
-                          *~ \
-                          *. \
-                          *.sln \
-                          *.sdf \
-                          *.tmp \
-                          *.vcxproj \
-                          *.filters \
-                          *.user \
-                          *.suo
+EXCLUDE_PATTERNS       = CMake* \
+                         *.txt \
+                         *.sh \
+                         *.orig \
+                         *.diff \
+                         diff \
+                         *~ \
+                         *. \
+                         *.sln \
+                         *.sdf \
+                         *.tmp \
+                         *.vcxproj \
+                         *.filters \
+                         *.user \
+                         *.suo
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -629,8 +761,11 @@ EXCLUDE_PATTERNS       =  CMake* \
 # wildcard * is used, a substring. Examples: ANamespace, AClass,
 # AClass::ANamespace, ANamespace::*Test
 
-# This could used to clean up the "class hierarchy" page
-EXCLUDE_SYMBOLS        = internal::* Flagged* *InnerIterator* DenseStorage<*
+EXCLUDE_SYMBOLS        = internal::* \
+                         Flagged* \
+                         *InnerIterator* \
+                         DenseStorage<* \
+                         
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or
 # directories that contain example code fragments that are included (see
@@ -641,7 +776,11 @@ EXAMPLE_PATH           = "${Eigen_SOURCE_DIR}/doc/snippets" \
                          "${Eigen_SOURCE_DIR}/doc/examples" \
                          "${Eigen_BINARY_DIR}/doc/examples" \
                          "${Eigen_SOURCE_DIR}/doc/special_examples" \
-                         "${Eigen_BINARY_DIR}/doc/special_examples"
+                         "${Eigen_BINARY_DIR}/doc/special_examples" \
+                         "${Eigen_SOURCE_DIR}/unsupported/doc/snippets" \
+                         "${Eigen_BINARY_DIR}/unsupported/doc/snippets" \
+                         "${Eigen_SOURCE_DIR}/unsupported/doc/examples" \
+                         "${Eigen_BINARY_DIR}/unsupported/doc/examples"
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
@@ -668,17 +807,20 @@ IMAGE_PATH             =
 # by executing (via popen()) the command <filter> <input-file>, where <filter>
 # is the value of the INPUT_FILTER tag, and <input-file> is the name of an
 # input file. Doxygen will then use the output that the filter program writes
-# to standard output.  If FILTER_PATTERNS is specified, this tag will be
+# to standard output.
+# If FILTER_PATTERNS is specified, this tag will be
 # ignored.
 
 INPUT_FILTER           =
 
 # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis.  Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match.  The filters are a list of the form:
+# basis.
+# Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match.
+# The filters are a list of the form:
 # pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
-# is applied to all files.
+# info on how filters are used. If FILTER_PATTERNS is empty or if
+# non of the patterns match the file name, INPUT_FILTER is applied.
 
 FILTER_PATTERNS        =
 
@@ -688,6 +830,14 @@ FILTER_PATTERNS        =
 
 FILTER_SOURCE_FILES    = NO
 
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
+# and it is also possible to disable source filtering for a specific pattern
+# using *.ext= (so without naming a filter). This option only has effect when
+# FILTER_SOURCE_FILES is enabled.
+
+FILTER_SOURCE_PATTERNS =
+
 #---------------------------------------------------------------------------
 # configuration options related to source browsing
 #---------------------------------------------------------------------------
@@ -706,7 +856,7 @@ INLINE_SOURCES         = NO
 
 # Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
 # doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C and C++ comments will always remain visible.
+# fragments. Normal C, C++ and Fortran comments will always remain visible.
 
 STRIP_CODE_COMMENTS    = YES
 
@@ -725,7 +875,8 @@ REFERENCES_RELATION    = YES
 # If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
 # and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
 # functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code.  Otherwise they will link to the documentstion.
+# link to the source code.
+# Otherwise they will link to the documentation.
 
 REFERENCES_LINK_SOURCE = YES
 
@@ -779,7 +930,7 @@ GENERATE_HTML          = YES
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `html' will be used as the default path.
 
-HTML_OUTPUT            = html
+HTML_OUTPUT            = "${Eigen_BINARY_DIR}/doc/html${EIGEN_DOXY_OUTPUT_DIRECTORY_SUFFIX}"
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for
 # each generated HTML page (for example: .htm,.php,.asp). If it is left blank
@@ -789,39 +940,89 @@ HTML_FILE_EXTENSION    = .html
 
 # The HTML_HEADER tag can be used to specify a personal HTML header for
 # each generated HTML page. If it is left blank doxygen will generate a
-# standard header.
+# standard header. Note that when using a custom header you are responsible
+#  for the proper inclusion of any scripts and style sheets that doxygen
+# needs, which is dependent on the configuration options used.
+# It is advised to generate a default header using "doxygen -w html
+# header.html footer.html stylesheet.css YourConfigFile" and then modify
+# that header. Note that the header is subject to change so you typically
+# have to redo this when upgrading to a newer version of doxygen or when
+# changing the value of configuration settings such as GENERATE_TREEVIEW!
 
-HTML_HEADER             = "${Eigen_BINARY_DIR}/doc/eigendoxy_header.html"
+HTML_HEADER            = "${Eigen_BINARY_DIR}/doc/eigendoxy_header.html"
 
 # The HTML_FOOTER tag can be used to specify a personal HTML footer for
 # each generated HTML page. If it is left blank doxygen will generate a
 # standard footer.
 
-# the footer has not been customized yet, so let's use the default one
-# ${Eigen_BINARY_DIR}/doc/eigendoxy_footer.html
-HTML_FOOTER             =
+HTML_FOOTER            = "${Eigen_BINARY_DIR}/doc/eigendoxy_footer.html"
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading
 # style sheet that is used by each HTML page. It can be used to
 # fine-tune the look of the HTML output. If the tag is left blank doxygen
 # will generate a default style sheet. Note that doxygen will try to copy
 # the style sheet file to the HTML output directory, so don't put your own
-# stylesheet in the HTML output directory as well, or it will be erased!
+# style sheet in the HTML output directory as well, or it will be erased!
 
-HTML_STYLESHEET         = "${Eigen_SOURCE_DIR}/doc/eigendoxy.css"
+HTML_STYLESHEET        = 
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that
+# the files will be copied as-is; there are no commands or markers available.
 
-HTML_ALIGN_MEMBERS     = YES
+HTML_EXTRA_FILES       = "${Eigen_SOURCE_DIR}/doc/eigendoxy.css"
 
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
-# of the generated HTML documentation.
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
+# Doxygen will adjust the colors in the style sheet and background images
+# according to this color. Hue is specified as an angle on a colorwheel,
+# see http://en.wikipedia.org/wiki/Hue for more information.
+# For instance the value 0 represents red, 60 is yellow, 120 is green,
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
+# The allowed range is 0 to 359.
+# The default is 220.
 
-GENERATE_HTMLHELP      = NO
+HTML_COLORSTYLE_HUE    = ${EIGEN_DOXY_HTML_COLORSTYLE_HUE}
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
+# the colors in the HTML output. For a value of 0 the output will use
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT    = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
+# the luminance component of the colors in the HTML output. Values below
+# 100 gradually make the output lighter, whereas values above 100 make
+# the output darker. The value divided by 100 is the actual gamma applied,
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA  = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting
+# this to NO can help when comparing the output of multiple runs.
+
+HTML_TIMESTAMP         = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded.
+
+HTML_DYNAMIC_SECTIONS  = YES
+
+# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of
+# entries shown in the various tree structured indices initially; the user
+# can expand and collapse entries dynamically later on. Doxygen will expand
+# the tree to such a level that at most the specified number of entries are
+# visible (unless a fully collapsed tree already exceeds this amount).
+# So setting the number of entries 1 will produce a full collapsed tree by
+# default. 0 is a special value representing an infinite number of entries
+# and will result in a full expanded tree by default.
+
+HTML_INDEX_NUM_ENTRIES = 100
 
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
@@ -831,6 +1032,8 @@ GENERATE_HTMLHELP      = NO
 # directory and running "make install" will install the docset in
 # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
 # it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
 
 GENERATE_DOCSET        = NO
 
@@ -848,13 +1051,22 @@ DOCSET_FEEDNAME        = "Doxygen generated docs"
 
 DOCSET_BUNDLE_ID       = org.doxygen.Project
 
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
-# documentation will contain sections that can be hidden and shown after the
-# page has loaded. For this to work a browser that supports
-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
 
-HTML_DYNAMIC_SECTIONS  = YES
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME  = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP      = NO
 
 # If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
 # be used to specify the file name of the resulting .chm file. You
@@ -893,33 +1105,102 @@ BINARY_TOC             = NO
 
 TOC_EXPAND             = NO
 
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
-# top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it.
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
+# that can be used as input for Qt's qhelpgenerator to generate a
+# Qt Compressed Help (.qch) of the generated HTML documentation.
 
-DISABLE_INDEX          = NO
+GENERATE_QHP           = NO
 
-# This tag can be used to set the number of enum values (range [1..20])
-# that doxygen will group on one line in the generated HTML documentation.
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
 
-ENUM_VALUES_PER_LINE   = 1
+QCH_FILE               =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE          = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
+# add. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME   =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
+# Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS  =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
+# Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS  =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION           =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
+#  will be generated, which together with the HTML files, form an Eclipse help
+# plugin. To install this plugin and make it available under the help contents
+# menu in Eclipse, the contents of the directory containing the HTML and XML
+# files needs to be copied into the plugins directory of eclipse. The name of
+# the directory within the plugins directory should be the same as
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
+# the help appears.
+
+GENERATE_ECLIPSEHELP   = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID         = org.doxygen.Project
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
+# at top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it. Since the tabs have the same information as the
+# navigation tree you can set this option to NO if you already set
+# GENERATE_TREEVIEW to YES.
+
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
-# If the tag value is set to FRAME, a side panel will be generated
+# If the tag value is set to YES, a side panel will be generated
 # containing a tree-like index structure (just like the one that
 # is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
-# probably better off using the HTML help feature. Other possible values
-# for this tag are: HIERARCHIES, which will generate the Groups, Directories,
-# and Class Hiererachy pages using a tree view instead of an ordered list;
-# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which
-# disables this behavior completely. For backwards compatibility with previous
-# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE
-# respectively.
-
-GENERATE_TREEVIEW      = NO
+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
+# Windows users are probably better off using the HTML help feature.
+# Since the tree basically has the same information as the tab index you
+# could consider to set DISABLE_INDEX to NO when enabling this option.
+
+GENERATE_TREEVIEW      = YES
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
+# (range [0,1..20]) that doxygen will group on one line in the generated HTML
+# documentation. Note that a value of 0 will completely suppress the enum
+# values from appearing in the overview section.
+
+ENUM_VALUES_PER_LINE   = 1
 
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
@@ -927,6 +1208,11 @@ GENERATE_TREEVIEW      = NO
 
 TREEVIEW_WIDTH         = 250
 
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
+# links to external symbols imported via tag files in a separate window.
+
+EXT_LINKS_IN_WINDOW    = NO
+
 # Use this tag to change the font size of Latex formulas included
 # as images in the HTML documentation. The default is 10. Note that
 # when you change the font size after a successful doxygen run you need
@@ -935,6 +1221,60 @@ TREEVIEW_WIDTH         = 250
 
 FORMULA_FONTSIZE       = 12
 
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are
+# not supported properly for IE 6.0, but are supported on all modern browsers.
+# Note that when changing this option you need to delete any form_*.png files
+# in the HTML output before the changes have effect.
+
+FORMULA_TRANSPARENT    = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
+# (see http://www.mathjax.org) which uses client side Javascript for the
+# rendering instead of using prerendered bitmaps. Use this if you do not
+# have LaTeX installed or if you want to formulas look prettier in the HTML
+# output. When enabled you may also need to install MathJax separately and
+# configure the path to it using the MATHJAX_RELPATH option.
+
+USE_MATHJAX            = NO
+
+# When MathJax is enabled you need to specify the location relative to the
+# HTML output directory using the MATHJAX_RELPATH option. The destination
+# directory should contain the MathJax.js script. For instance, if the mathjax
+# directory is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to
+# the MathJax Content Delivery Network so you can quickly see the result without
+# installing MathJax.
+# However, it is strongly recommended to install a local
+# copy of MathJax from http://www.mathjax.org before deployment.
+
+MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
+# names that should be enabled during MathJax rendering.
+
+MATHJAX_EXTENSIONS     =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
+# for the HTML output. The underlying search engine uses javascript
+# and DHTML and should work on any modern browser. Note that when using
+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
+# (GENERATE_DOCSET) there is already a search function so this one should
+# typically be disabled. For large projects the javascript based search engine
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE           = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a PHP enabled web server instead of at the web client
+# using Javascript. Doxygen will generate the search PHP script and index
+# file to put on the web server. The advantage of the server
+# based approach is that it scales better to large projects and allows
+# full text search. The disadvantages are that it is more difficult to setup
+# and does not have live searching capabilities.
+
+SERVER_BASED_SEARCH    = NO
+
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
@@ -952,6 +1292,9 @@ LATEX_OUTPUT           = latex
 
 # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
 # invoked. If left blank `latex' will be used as the default command name.
+# Note that when enabling USE_PDFLATEX this option is only used for
+# generating bitmaps for formulas in the HTML output, but not in the
+# Makefile that is written to the output directory.
 
 LATEX_CMD_NAME         = latex
 
@@ -968,7 +1311,7 @@ MAKEINDEX_CMD_NAME     = makeindex
 COMPACT_LATEX          = NO
 
 # The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, a4wide, letter, legal and
+# by the printer. Possible values are: a4, letter, legal and
 # executive. If left blank a4wide will be used.
 
 PAPER_TYPE             = a4wide
@@ -986,6 +1329,13 @@ EXTRA_PACKAGES         = amssymb \
 
 LATEX_HEADER           =
 
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
+# the generated latex document. The footer should contain everything after
+# the last chapter. If it is left blank doxygen will generate a
+# standard footer. Notice: only use this tag if you know what you are doing!
+
+LATEX_FOOTER           =
+
 # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
 # is prepared for conversion to pdf (using ps2pdf). The pdf file will
 # contain links (just like the HTML output) instead of page references
@@ -1012,6 +1362,19 @@ LATEX_BATCHMODE        = NO
 
 LATEX_HIDE_INDICES     = NO
 
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
+# source code with syntax highlighting in the LaTeX output.
+# Note that which sources are shown also depends on other settings
+# such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE      = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
+# http://en.wikipedia.org/wiki/BibTeX for more info.
+
+LATEX_BIB_STYLE        = plain
+
 #---------------------------------------------------------------------------
 # configuration options related to the RTF output
 #---------------------------------------------------------------------------
@@ -1043,7 +1406,7 @@ COMPACT_RTF            = NO
 
 RTF_HYPERLINKS         = NO
 
-# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# Load style sheet definitions from file. Syntax is similar to doxygen's
 # config file, i.e. a series of assignments. You only have to provide
 # replacements, missing definitions are set to their default value.
 
@@ -1148,8 +1511,10 @@ GENERATE_PERLMOD       = NO
 PERLMOD_LATEX          = NO
 
 # If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader.  This is useful
-# if you want to understand what is going on.  On the other hand, if this
+# nicely formatted so it can be parsed by a human reader.
+# This is useful
+# if you want to understand what is going on.
+# On the other hand, if this
 # tag is set to NO the size of the Perl module output will be much smaller
 # and Perl will parse it just the same.
 
@@ -1186,7 +1551,7 @@ MACRO_EXPANSION        = YES
 EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
+# pointed to by INCLUDE_PATH will be searched when a #include is found.
 
 SEARCH_INCLUDES        = YES
 
@@ -1194,7 +1559,7 @@ SEARCH_INCLUDES        = YES
 # contain include files that are not input files but should be processed by
 # the preprocessor.
 
-INCLUDE_PATH           = "${Eigen_SOURCE_DIR}/Eigen/src/plugins" 
+INCLUDE_PATH           = "${Eigen_SOURCE_DIR}/Eigen/src/plugins"
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the
@@ -1216,29 +1581,30 @@ PREDEFINED             = EIGEN_EMPTY_STRUCT \
                          EIGEN_VECTORIZE \
                          EIGEN_QT_SUPPORT \
                          EIGEN_STRONG_INLINE=inline \
-                         EIGEN2_SUPPORT_STAGE=99
+                         "EIGEN2_SUPPORT_STAGE=99" \
+                         "EIGEN_MAKE_CWISE_BINARY_OP(METHOD,FUNCTOR)=template<typename OtherDerived> const CwiseBinaryOp<FUNCTOR<Scalar>, const Derived, const OtherDerived> METHOD(const EIGEN_CURRENT_STORAGE_BASE_CLASS<OtherDerived> &other) const;" \
+                         "EIGEN_CWISE_PRODUCT_RETURN_TYPE(LHS,RHS)=CwiseBinaryOp<internal::scalar_product_op<typename LHS::Scalar, typename RHS::Scalar >, const LHS, const RHS>"
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
 # this tag can be used to specify a list of macro names that should be expanded.
 # The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition.
+# Use the PREDEFINED tag if you want to use a different macro definition that
+# overrules the definition found in the source code.
 
 EXPAND_AS_DEFINED      = EIGEN_MAKE_TYPEDEFS \
                          EIGEN_MAKE_FIXED_TYPEDEFS \
                          EIGEN_MAKE_TYPEDEFS_ALL_SIZES \
-                         EIGEN_MAKE_CWISE_BINARY_OP \
                          EIGEN_CWISE_UNOP_RETURN_TYPE \
                          EIGEN_CWISE_BINOP_RETURN_TYPE \
-                         EIGEN_CWISE_PRODUCT_RETURN_TYPE \
                          EIGEN_CURRENT_STORAGE_BASE_CLASS \
+                         EIGEN_MATHFUNC_IMPL \
                          _EIGEN_GENERIC_PUBLIC_INTERFACE \
                          EIGEN2_SUPPORT
 
 # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all function-like macros that are alone
-# on a line, have an all uppercase name, and do not end with a semicolon. Such
-# function macros are typically used for boiler-plate code, and will confuse
-# the parser if not removed.
+# doxygen's preprocessor will remove all references to function-like macros
+# that are alone on a line, have an all uppercase name, and do not end with a
+# semicolon, because these will confuse the parser if not removed.
 
 SKIP_FUNCTION_MACROS   = YES
 
@@ -1246,27 +1612,26 @@ SKIP_FUNCTION_MACROS   = YES
 # Configuration::additions related to external references
 #---------------------------------------------------------------------------
 
-# The TAGFILES option can be used to specify one or more tagfiles.
-# Optionally an initial location of the external documentation
-# can be added for each tagfile. The format of a tag file without
-# this location is as follows:
-#   TAGFILES = file1 file2 ...
+# The TAGFILES option can be used to specify one or more tagfiles. For each
+# tag file the location of the external documentation should be added. The
+# format of a tag file without this location is as follows:
+#
+# TAGFILES = file1 file2 ...
 # Adding location for the tag files is done as follows:
-#   TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths or
-# URLs. If a location is present for each tag, the installdox tool
-# does not have to be run to correct the links.
-# Note that each tag file must have a unique name
-# (where the name does NOT include the path)
-# If a tag file is not located in the directory in which doxygen
-# is run, you must also specify the path to the tagfile here.
+#
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths
+# or URLs. Note that each tag file must have a unique name (where the name does
+# NOT include the path). If a tag file is not located in the directory in which
+# doxygen is run, you must also specify the path to the tagfile here.
 
-TAGFILES               = "${Eigen_BINARY_DIR}/doc/eigen-unsupported.doxytags"=unsupported
+TAGFILES               = ${EIGEN_DOXY_TAGFILES}
+# "${Eigen_BINARY_DIR}/doc/eigen-unsupported.doxytags =unsupported"
 
 # When a file name is specified after GENERATE_TAGFILE, doxygen will create
 # a tag file that is based on the input files it reads.
 
-GENERATE_TAGFILE       = "${Eigen_BINARY_DIR}/doc/eigen.doxytags"
+GENERATE_TAGFILE       = "${Eigen_BINARY_DIR}/doc/${EIGEN_DOXY_PROJECT_NAME}.doxytags"
 
 # If the ALLEXTERNALS tag is set to YES all external classes will be listed
 # in the class index. If set to NO only the inherited external classes
@@ -1292,9 +1657,8 @@ PERL_PATH              = /usr/bin/perl
 # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
 # generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
 # or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option is superseded by the HAVE_DOT option below. This is only a
-# fallback. It is recommended to install and use dot, since it yields more
-# powerful graphs.
+# this option also works with HAVE_DOT disabled, but it is recommended to
+# install and use dot, since it yields more powerful graphs.
 
 CLASS_DIAGRAMS         = YES
 
@@ -1320,28 +1684,38 @@ HIDE_UNDOC_RELATIONS   = NO
 
 HAVE_DOT               = YES
 
-# By default doxygen will write a font called FreeSans.ttf to the output
-# directory and reference it in all dot files that doxygen generates. This
-# font does not include all possible unicode characters however, so when you need
-# these (or just want a differently looking font) you can specify the font name
-# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
-# which can be done by putting it in a standard location or by setting the
-# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
-# containing the font.
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
+# allowed to run in parallel. When set to 0 (the default) doxygen will
+# base this on the number of processors available in the system. You can set it
+# explicitly to a value larger than 0 to get control over the balance
+# between CPU load and processing speed.
+
+DOT_NUM_THREADS        = 0
+
+# By default doxygen will use the Helvetica font for all dot files that
+# doxygen generates. When you want a differently looking font you can specify
+# the font name using DOT_FONTNAME. You need to make sure dot is able to find
+# the font, which can be done by putting it in a standard location or by setting
+# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
+# directory containing the font.
 
 DOT_FONTNAME           = FreeSans
 
-# By default doxygen will tell dot to use the output directory to look for the
-# FreeSans.ttf font (which doxygen will put there itself). If you specify a
-# different font using DOT_FONTNAME you can set the path where dot
-# can find it using this tag.
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE           = 10
+
+# By default doxygen will tell dot to use the Helvetica font.
+# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
+# set the path where dot can find it.
 
 DOT_FONTPATH           =
 
 # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
 # will generate a graph for each documented class showing the direct and
 # indirect inheritance relations. Setting this tag to YES will force the
-# the CLASS_DIAGRAMS tag to NO.
+# CLASS_DIAGRAMS tag to NO.
 
 CLASS_GRAPH            = YES
 
@@ -1363,6 +1737,15 @@ GROUP_GRAPHS           = NO
 
 UML_LOOK               = YES
 
+# If the UML_LOOK tag is enabled, the fields and methods are shown inside
+# the class node. If there are many fields or methods and many nodes the
+# graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
+# threshold limits the number of items for each type to make the size more
+# managable. Set this to 0 for no limit. Note that the threshold may be
+# exceeded by 50% before the limit is enforced.
+
+UML_LIMIT_NUM_FIELDS   = 10
+
 # If set to YES, the inheritance and collaboration graphs will show the
 # relations between templates and their instances.
 
@@ -1399,11 +1782,11 @@ CALL_GRAPH             = NO
 CALLER_GRAPH           = NO
 
 # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will graphical hierarchy of all classes instead of a textual one.
+# will generate a graphical hierarchy of all classes instead of a textual one.
 
 GRAPHICAL_HIERARCHY    = NO
 
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES
 # then doxygen will show the dependencies a directory has on other directories
 # in a graphical way. The dependency relations are determined by the #include
 # relations between the files in the directories.
@@ -1411,11 +1794,22 @@ GRAPHICAL_HIERARCHY    = NO
 DIRECTORY_GRAPH        = NO
 
 # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are png, jpg, or gif
-# If left blank png will be used.
+# generated by dot. Possible values are svg, png, jpg, or gif.
+# If left blank png will be used. If you choose svg you need to set
+# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
+# visible in IE 9+ (other browsers do not have this requirement).
 
 DOT_IMAGE_FORMAT       = png
 
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+# Note that this requires a modern browser other than Internet Explorer.
+# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
+# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
+# visible. Older versions of IE do not have SVG support.
+
+INTERACTIVE_SVG        = NO
+
 # The tag DOT_PATH can be used to specify the path where the dot tool can be
 # found. If left blank, it is assumed the dot tool can be found in the path.
 
@@ -1427,6 +1821,12 @@ DOT_PATH               =
 
 DOTFILE_DIRS           =
 
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the
+# \mscfile command).
+
+MSCFILE_DIRS           =
+
 # The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
 # nodes that will be shown in the graph. If the number of nodes in a graph
 # becomes larger than this value, doxygen will truncate the graph, which is
@@ -1448,10 +1848,10 @@ DOT_GRAPH_MAX_NODES    = 50
 MAX_DOT_GRAPH_DEPTH    = 0
 
 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is enabled by default, which results in a transparent
-# background. Warning: Depending on the platform used, enabling this option
-# may lead to badly anti-aliased labels on the edges of a graph (i.e. they
-# become hard to read).
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
 
 DOT_TRANSPARENT        = NO
 
@@ -1473,12 +1873,3 @@ GENERATE_LEGEND        = YES
 # the various graphs.
 
 DOT_CLEANUP            = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to the search engine
-#---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be
-# used. If set to NO the values of all tags below this one will be ignored.
-
-SEARCHENGINE           = NO
diff --git a/doc/I05_FixedSizeVectorizable.dox b/doc/FixedSizeVectorizable.dox
index 192ea7406..8ae135173 100644
--- a/doc/I05_FixedSizeVectorizable.dox
+++ b/doc/FixedSizeVectorizable.dox
@@ -1,6 +1,6 @@
 namespace Eigen {
 
-/** \page TopicFixedSizeVectorizable Fixed-size vectorizable Eigen objects
+/** \eigenManualPage TopicFixedSizeVectorizable Fixed-size vectorizable Eigen objects
 
 The goal of this page is to explain what we mean by "fixed-size vectorizable".
 
diff --git a/doc/I13_FunctionsTakingEigenTypes.dox b/doc/FunctionsTakingEigenTypes.dox
index f9e6fafed..152dda47d 100644
--- a/doc/I13_FunctionsTakingEigenTypes.dox
+++ b/doc/FunctionsTakingEigenTypes.dox
@@ -1,23 +1,18 @@
 namespace Eigen {
 
-/** \page TopicFunctionTakingEigenTypes Writing Functions Taking Eigen Types as Parameters
+/** \page TopicFunctionTakingEigenTypes Writing Functions Taking %Eigen Types as Parameters
 
-Eigen's use of expression templates results in potentially every expression being of a different type. If you pass such an expression to a function taking a parameter of type Matrix, your expression will implicitly be evaluated into a temporary Matrix, which will then be passed to the function. This means that you lose the benefit of expression templates. Concretely, this has two drawbacks:
+%Eigen's use of expression templates results in potentially every expression being of a different type. If you pass such an expression to a function taking a parameter of type Matrix, your expression will implicitly be evaluated into a temporary Matrix, which will then be passed to the function. This means that you lose the benefit of expression templates. Concretely, this has two drawbacks:
  \li The evaluation into a temporary may be useless and inefficient;
  \li This only allows the function to read from the expression, not to write to it.
 
-Fortunately, all this myriad of expression types have in common that they all inherit a few common, templated base classes. By letting your function take templated parameters of these base types, you can let them play nicely with Eigen's expression templates.
+Fortunately, all this myriad of expression types have in common that they all inherit a few common, templated base classes. By letting your function take templated parameters of these base types, you can let them play nicely with %Eigen's expression templates.
 
-<b>Table of contents</b>
-  - \ref TopicFirstExamples
-  - \ref TopicPlainFunctionsWorking
-  - \ref TopicPlainFunctionsFailing
-  - \ref TopicResizingInGenericImplementations
-  - \ref TopicSummary
+\eigenAutoToc
 
 \section TopicFirstExamples Some First Examples
 
-This section will provide simple examples for different types of objects Eigen is offering. Before starting with the actual examples, we need to recapitulate which base objects we can work with (see also \ref TopicClassHierarchy).
+This section will provide simple examples for different types of objects %Eigen is offering. Before starting with the actual examples, we need to recapitulate which base objects we can work with (see also \ref TopicClassHierarchy).
 
  \li MatrixBase: The common base class for all dense matrix expressions (as opposed to array expressions, as opposed to sparse and special matrix classes). Use it in functions that are meant to work only on dense matrices.
  \li ArrayBase: The common base class for all dense array expressions (as opposed to matrix expressions, etc). Use it in functions that are meant to work only on arrays.
@@ -25,7 +20,7 @@ This section will provide simple examples for different types of objects Eigen i
  \li EigenBase: The base class unifying all types of objects that can be evaluated into dense matrices or arrays, for example special matrix classes such as diagonal matrices, permutation matrices, etc. It can be used in functions that are meant to work on any such general type.
 
 <b> %EigenBase Example </b><br/><br/>
-Prints the dimensions of the most generic object present in Eigen. It coulde be any matrix expressions, any dense or sparse matrix and any array.
+Prints the dimensions of the most generic object present in %Eigen. It could be any matrix expressions, any dense or sparse matrix and any array.
 <table class="example">
 <tr><th>Example:</th><th>Output:</th></tr>
 <tr><td>
@@ -81,9 +76,42 @@ where the first argument \c v1 is a vector and the second argument \c 2*v2 is an
 
 These examples are just intended to give the reader a first impression of how functions can be written which take a plain and constant Matrix or Array argument. They are also intended to give the reader an idea about the most common base classes being the optimal candidates for functions. In the next section we will look in more detail at an example and the different ways it can be implemented, while discussing each implementation's problems and advantages. For the discussion below, Matrix and Array as well as MatrixBase and ArrayBase can be exchanged and all arguments still hold.
 
+
+\section TopicUsingRefClass How to write generic, but non-templated function?
+
+In all the previous examples, the functions had to be template functions. This approach allows to write very generic code, but it is often desirable to write non templated function and still keep some level of genericity to avoid stupid copies of the arguments. The typical example is to write functions accepting both a MatrixXf or a block of a MatrixXf. This exactly the purpose of the Ref class. Here is a simple example:
+
+<table class="example">
+<tr><th>Example:</th><th>Output:</th></tr>
+<tr><td>
+\include function_taking_ref.cpp
+</td>
+<td>
+\verbinclude function_taking_ref.out
+</td></tr></table>
+In the first two calls to inv_cond, no copy occur because the memory layout of the arguments matches the memory layout accepted by Ref<MatrixXf>. However, in the last call, we have a generic expression that will be automatically evaluated into a temporary MatrixXf by the Ref<> object.
+
+A Ref object can also be writable. Here is an example of a function computing the covariance matrix of two input matrices where each row is an observation:
+\code
+void cov(const Ref<const MatrixXf> x, const Ref<const MatrixXf> y, Ref<MatrixXf> C)
+{
+  const float num_observations = static_cast<float>(x.rows());
+  const RowVectorXf x_mean = x.colwise().sum() / num_observations;
+  const RowVectorXf y_mean = y.colwise().sum() / num_observations;
+  C = (x.rowwise() - x_mean).transpose() * (y.rowwise() - y_mean) / num_observations;
+}
+\endcode
+and here are two examples calling cov without any copy:
+\code
+MatrixXf m1, m2, m3
+cov(m1, m2, m3);
+cov(m1.leftCols<3>(), m2.leftCols<3>(), m3.topLeftCorner<3,3>());
+\endcode
+The Ref<> class has two other optional template arguments allowing to control the kind of memory layout that can be accepted without any copy. See the class Ref documentation for the details.
+
 \section TopicPlainFunctionsWorking In which cases do functions taking plain Matrix or Array arguments work?
 
-Let's assume one wants to write a function computing the covariance matrix of two input matrices where each row is an observation. The implementation of this function might look like this
+Without using template functions, and without the Ref class, a naive implementation of the previous cov function might look like this
 \code
 MatrixXf cov(const MatrixXf& x, const MatrixXf& y)
 {
@@ -93,7 +121,7 @@ MatrixXf cov(const MatrixXf& x, const MatrixXf& y)
   return (x.rowwise() - x_mean).transpose() * (y.rowwise() - y_mean) / num_observations;
 }
 \endcode
-and contrary to what one might think at first, this implementation is fine unless you require a genric implementation that works with double matrices too and unless you do not care about temporary objects. Why is that the case? Where are temporaries involved? How can code as given below compile?
+and contrary to what one might think at first, this implementation is fine unless you require a generic implementation that works with double matrices too and unless you do not care about temporary objects. Why is that the case? Where are temporaries involved? How can code as given below compile?
 \code
 MatrixXf x,y,z;
 MatrixXf C = cov(x,y+z);
@@ -102,6 +130,7 @@ In this special case, the example is fine and will be working because both param
 
 \b Note: Functions taking \e const references to Matrix (or Array) can process expressions at the cost of temporaries.
 
+
 \section TopicPlainFunctionsFailing In which cases do functions taking a plain Matrix or Array argument fail?
 
 Here, we consider a slightly modified version of the function given above. This time, we do not want to return the result but pass an additional non-const paramter which allows us to store the result. A first naive implementation might look as follows.
@@ -154,7 +183,7 @@ MatrixXf y = MatrixXf::Random(100,3);
 MatrixXf C;
 cov(x, y, C);
 \endcode
-This is not the case anymore, when we are using an implementation taking MatrixBase as a parameter. In general, Eigen supports automatic resizing but it is not possible to do so on expressions. Why should resizing of a matrix Block be allowed? It is a reference to a sub-matrix and we definitely don't want to resize that. So how can we incorporate resizing if we cannot resize on MatrixBase? The solution is to resize the derived object as in this implementation.
+This is not the case anymore, when we are using an implementation taking MatrixBase as a parameter. In general, %Eigen supports automatic resizing but it is not possible to do so on expressions. Why should resizing of a matrix Block be allowed? It is a reference to a sub-matrix and we definitely don't want to resize that. So how can we incorporate resizing if we cannot resize on MatrixBase? The solution is to resize the derived object as in this implementation.
 \code
 template <typename Derived, typename OtherDerived>
 void cov(const MatrixBase<Derived>& x, const MatrixBase<Derived>& y, MatrixBase<OtherDerived> const & C_)
diff --git a/doc/I02_HiPerformance.dox b/doc/HiPerformance.dox
index ac1c2ca2b..ab6cdfd44 100644
--- a/doc/I02_HiPerformance.dox
+++ b/doc/HiPerformance.dox
@@ -79,7 +79,7 @@ temp = m2 * m3;
 m1 += temp.adjoint(); \endcode</td>
 <td>\code
 m1.noalias() += m3.adjoint()
-              * m2.adjoint(); \endcode</td>
+*              * m2.adjoint(); \endcode</td>
 <td>This is because the product expression has the EvalBeforeNesting bit which
     enforces the evaluation of the product by the Tranpose expression.</td>
 </tr>
diff --git a/doc/I10_Assertions.dox b/doc/I10_Assertions.dox
deleted file mode 100644
index d5697fcee..000000000
--- a/doc/I10_Assertions.dox
+++ /dev/null
@@ -1,13 +0,0 @@
-namespace Eigen {
-
-/** \page TopicAssertions Assertions
-
-
-TODO: write this dox page!
-
-Is linked from the tutorial on matrix arithmetic.
-
-\sa Section \ref TopicPreprocessorDirectivesAssertions on page \ref TopicPreprocessorDirectives.
-
-*/
-}
diff --git a/doc/I03_InsideEigenExample.dox b/doc/InsideEigenExample.dox
index 3245a01c0..ed053c69d 100644
--- a/doc/I03_InsideEigenExample.dox
+++ b/doc/InsideEigenExample.dox
@@ -2,12 +2,7 @@ namespace Eigen {
 
 /** \page TopicInsideEigenExample What happens inside Eigen, on a simple example
 
-\b Table \b of \b contents
-  - \ref WhyInteresting
-  - \ref ConstructingVectors
-  - \ref ConstructionOfSumXpr
-  - \ref Assignment
-\n
+\eigenAutoToc
 
 <hr>
 
diff --git a/doc/Manual.dox b/doc/Manual.dox
new file mode 100644
index 000000000..3367982ca
--- /dev/null
+++ b/doc/Manual.dox
@@ -0,0 +1,159 @@
+
+// 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 SparseQR_Module
+    \ingroup Sparse_Reference */
+/** \addtogroup IterativeLinearSolvers_Module
+    \ingroup Sparse_Reference */
+/** \addtogroup Sparse_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 */
+}
diff --git a/doc/Overview.dox b/doc/Overview.dox
index 2657c85bc..9ab96233a 100644
--- a/doc/Overview.dox
+++ b/doc/Overview.dox
@@ -1,59 +1,27 @@
 namespace Eigen {
 
-o /** \mainpage Eigen
-
-<div class="eimainmenu">
-    \ref GettingStarted       "Getting started"
-  | \ref TutorialMatrixClass  "Tutorial"
-  | \ref QuickRefPage         "Short reference"
-</div>
+/** \mainpage notitle
 
 This is the API documentation for Eigen3. You can <a href="eigen-doc.tgz">download</a> it as a tgz archive for offline reading.
 
-Eigen2 users: here is a \ref Eigen2ToEigen3 guide to help porting your application.
-
-For a first contact with Eigen, the best place is to have a look at the \ref GettingStarted "tutorial". The \ref QuickRefPage "short reference" page gives you a quite complete description of the API in a very condensed format that is specially useful to recall the syntax of a particular feature, or to have a quick look at the API. For Matlab users, there is also a <a href="AsciiQuickReference.txt">ASCII quick reference</a> with Matlab translations. The \e Modules and \e Classes tabs at the top of this page give you access to the API documentation of individual classes and functions.
-
-\b Table \b of \b contents
-  - \ref Eigen2ToEigen3
-  - \ref GettingStarted
-  - \b Tutorial
-    - \ref TutorialMatrixClass
-    - \ref TutorialMatrixArithmetic
-    - \ref TutorialArrayClass
-    - \ref TutorialBlockOperations
-    - \ref TutorialAdvancedInitialization
-    - \ref TutorialLinearAlgebra
-    - \ref TutorialReductionsVisitorsBroadcasting
-    - \ref TutorialGeometry
-    - \ref TutorialSparse
-    - \ref TutorialMapClass
-  - \ref QuickRefPage
-  - <b>Advanced topics</b>
-    - \ref TopicAliasing
-    - \ref TopicLazyEvaluation
-    - \ref TopicLinearAlgebraDecompositions
-    - \ref TopicCustomizingEigen
-    - \ref TopicMultiThreading
-    - \ref TopicPreprocessorDirectives
-    - \ref TopicStorageOrders
-    - \ref TopicInsideEigenExample
-    - \ref TopicWritingEfficientProductExpression
-    - \ref TopicClassHierarchy
-    - \ref TopicFunctionTakingEigenTypes
-    - \ref TopicTemplateKeyword
-    - \ref TopicUsingIntelMKL
-  - <b>Topics related to alignment issues</b>
-    - \ref TopicUnalignedArrayAssert
-    - \ref TopicFixedSizeVectorizable
-    - \ref TopicStlContainers
-    - \ref TopicStructHavingEigenMembers
-    - \ref TopicPassingByValue
-    - \ref TopicWrongStackAlignment
+You're already an Eigen2 user? Here is a \link Eigen2ToEigen3 Eigen2 to Eigen3 guide \endlink to help porting your application.
+
+For a first contact with Eigen, the best place is to have a look at the \link GettingStarted getting started \endlink page that show you how to write and compile your first program with Eigen.
+
+Then, the \b quick \b reference \b pages give you a quite complete description of the API in a very condensed format that is specially useful to recall the syntax of a particular feature, or to have a quick look at the API. They currently cover the two following feature sets, and more will come in the future:
+  - \link QuickRefPage [QuickRef] Dense matrix and array manipulations \endlink
+  - \link SparseQuickRefPage [QuickRef] Sparse linear algebra \endlink
+
+You're a MatLab user? There is also a <a href="AsciiQuickReference.txt">short ASCII reference</a> with Matlab translations.
   
-   
+The \b main \b documentation is organized into \em chapters covering different domains of features.
+They are themselves composed of \em user \em manual pages describing the different features in a comprehensive way, and \em reference pages that gives you access to the API documentation through the related Eigen's \em modules and \em classes.
+
+Under the  \subpage UserManual_Generalities section, you will find documentation on more general topics such as preprocessor directives, controlling assertions, multi-threading, MKL support, some Eigen's internal insights, and much more...
+
+Finally, do not miss the search engine, useful to quickly get to the documentation of a given class or function.
 
-Want more? Checkout the \ref Unsupported_modules "unsupported modules" <a href="unsupported/index.html">documentation</a>.
+Want more? Checkout the <a href="unsupported/index.html">\em unsupported \em modules </a> documentation.
 
 */
 
diff --git a/doc/D07_PassingByValue.dox b/doc/PassingByValue.dox
index b1e5e683b..bf4d0ef4b 100644
--- a/doc/D07_PassingByValue.dox
+++ b/doc/PassingByValue.dox
@@ -1,6 +1,6 @@
 namespace Eigen {
 
-/** \page TopicPassingByValue Passing Eigen objects by value to functions
+/** \eigenManualPage TopicPassingByValue Passing Eigen objects by value to functions
 
 Passing objects by value is almost always a very bad idea in C++, as this means useless copies, and one should pass them by reference instead.
 
diff --git a/doc/I14_PreprocessorDirectives.dox b/doc/PreprocessorDirectives.dox
index f29f0720c..8a2968ebb 100644
--- a/doc/I14_PreprocessorDirectives.dox
+++ b/doc/PreprocessorDirectives.dox
@@ -7,12 +7,7 @@ should be defined before any %Eigen headers are included. Often they are best se
 
 This page lists the preprocesor tokens recognised by %Eigen.
 
-<b>Table of contents</b>
-  - \ref TopicPreprocessorDirectivesMajor
-  - \ref TopicPreprocessorDirectivesAssertions
-  - \ref TopicPreprocessorDirectivesPerformance
-  - \ref TopicPreprocessorDirectivesPlugins
-  - \ref TopicPreprocessorDirectivesDevelopers
+\eigenAutoToc
 
 
 \section TopicPreprocessorDirectivesMajor Macros with major effects
@@ -29,10 +24,14 @@ are doing.
    Eigen3; see \ref Eigen2SupportModes.
  - \b EIGEN_DEFAULT_DENSE_INDEX_TYPE - the type for column and row indices in matrices, vectors and array
    (DenseBase::Index). Set to \c std::ptrdiff_t by default.
- - \b EIGEN_DEFAULT_IO_FORMAT - the IOFormat to use when printing a matrix if no #IOFormat is specified.
-   Defaults to the #IOFormat constructed by the default constructor IOFormat().
+ - \b EIGEN_DEFAULT_IO_FORMAT - the IOFormat to use when printing a matrix if no %IOFormat is specified.
+   Defaults to the %IOFormat constructed by the default constructor IOFormat::IOFormat().
  - \b EIGEN_INITIALIZE_MATRICES_BY_ZERO - if defined, all entries of newly constructed matrices and arrays are
-   initializes to zero, as are new entries in matrices and arrays after resizing. Not defined by default.
+   initialized to zero, as are new entries in matrices and arrays after resizing. Not defined by default.
+ - \b EIGEN_INITIALIZE_MATRICES_BY_NAN - if defined, all entries of newly constructed matrices and arrays are
+   initialized to NaN, as are new entries in matrices and arrays after resizing. This option is especially
+   useful for debugging purpose, though a memory tool like <a href="http://valgrind.org/">valgrind</a> is
+   preferable. Not defined by default.
  - \b EIGEN_NO_AUTOMATIC_RESIZING - if defined, the matrices (or arrays) on both sides of an assignment 
    <tt>a = b</tt> have to be of the same size; otherwise, %Eigen automatically resizes \c a so that it is of
    the correct size. Not defined by default.
@@ -56,18 +55,26 @@ run time. However, these assertions do cost time and can thus be turned off.
 
 \section TopicPreprocessorDirectivesPerformance Alignment, vectorization and performance tweaking
 
+ - \b EIGEN_MALLOC_ALREADY_ALIGNED - Can be set to 0 or 1 to tell whether default system malloc already
+   returns aligned buffers. In not defined, then this information is automatically deduced from the compiler
+   and system preprocessor tokens.
  - \b EIGEN_DONT_ALIGN - disables alignment completely. %Eigen will not try to align its objects and does not
    expect that any objects passed to it are aligned. This will turn off vectorization. Not defined by default.
  - \b EIGEN_DONT_ALIGN_STATICALLY - disables alignment of arrays on the stack. Not defined by default, unless
    \c EIGEN_DONT_ALIGN is defined.
+ - \b EIGEN_DONT_PARALLELIZE - if defined, this disables multi-threading. This is only relevant if you enabled OpenMP.
+   See \ref TopicMultiThreading for details.
  - \b EIGEN_DONT_VECTORIZE - disables explicit vectorization when defined. Not defined by default, unless 
    alignment is disabled by %Eigen's platform test or the user defining \c EIGEN_DONT_ALIGN.
- - \b EIGEN_FAST_MATH - enables some optimizations which might affect the accuracy of the result. The only
-   optimization this currently includes is single precision sin() and cos() in the present of SSE
-   vectorization. Defined by default. 
+ - \b EIGEN_FAST_MATH - enables some optimizations which might affect the accuracy of the result. This currently
+   enables the SSE vectorization of sin() and cos(), and speedups sqrt() for single precision. Defined to 1 by default.
+   Define it to 0 to disable.
  - \b EIGEN_UNROLLING_LIMIT - defines the size of a loop to enable meta unrolling. Set it to zero to disable
    unrolling. The size of a loop here is expressed in %Eigen's own notion of "number of FLOPS", it does not
-   correspond to the number of iterations or the number of instructions. The default is value 100. 
+   correspond to the number of iterations or the number of instructions. The default is value 100.
+ - \b EIGEN_STACK_ALLOCATION_LIMIT - defines the maximum bytes for a buffer to be allocated on the stack. For internal
+   temporary buffers, dynamic memory allocation is employed as a fall back. For fixed-size matrices or arrays, exceeding
+   this threshold raises a compile time assertion. Use 0 to set no limit. Default is 128 KB.
 
 
 \section TopicPreprocessorDirectivesPlugins Plugins
diff --git a/doc/QuickReference.dox b/doc/QuickReference.dox
index 3310d390a..a4be0f68a 100644
--- a/doc/QuickReference.dox
+++ b/doc/QuickReference.dox
@@ -1,18 +1,8 @@
 namespace Eigen {
 
-/** \page QuickRefPage Quick reference guide
-
-\b Table \b of \b contents
-  - \ref QuickRef_Headers
-  - \ref QuickRef_Types
-  - \ref QuickRef_Map
-  - \ref QuickRef_ArithmeticOperators
-  - \ref QuickRef_Coeffwise
-  - \ref QuickRef_Reductions
-  - \ref QuickRef_Blocks
-  - \ref QuickRef_Misc
-  - \ref QuickRef_DiagTriSymm
-\n
+/** \eigenManualPage QuickRefPage Quick reference guide
+
+\eigenAutoToc
 
 <hr>
 
@@ -31,7 +21,7 @@ The Eigen library is divided in a Core module and several additional modules. Ea
 <tr><td>\link SVD_Module SVD \endlink</td><td>\code#include <Eigen/SVD>\endcode</td><td>SVD decomposition with least-squares solver (JacobiSVD)</td></tr>
 <tr class="alt"><td>\link QR_Module QR \endlink</td><td>\code#include <Eigen/QR>\endcode</td><td>QR decomposition with solver (HouseholderQR, ColPivHouseholderQR, FullPivHouseholderQR)</td></tr>
 <tr><td>\link Eigenvalues_Module Eigenvalues \endlink</td><td>\code#include <Eigen/Eigenvalues>\endcode</td><td>Eigenvalue, eigenvector decompositions (EigenSolver, SelfAdjointEigenSolver, ComplexEigenSolver)</td></tr>
-<tr class="alt"><td>\link Sparse_Module Sparse \endlink</td><td>\code#include <Eigen/Sparse>\endcode</td><td>%Sparse matrix storage and related basic linear algebra (SparseMatrix, DynamicSparseMatrix, SparseVector)</td></tr>
+<tr class="alt"><td>\link Sparse_modules Sparse \endlink</td><td>\code#include <Eigen/Sparse>\endcode</td><td>%Sparse matrix storage and related basic linear algebra (SparseMatrix, DynamicSparseMatrix, SparseVector)</td></tr>
 <tr><td></td><td>\code#include <Eigen/Dense>\endcode</td><td>Includes Core, Geometry, LU, Cholesky, SVD, QR, and Eigenvalues header files</td></tr>
 <tr class="alt"><td></td><td>\code#include <Eigen/Eigen>\endcode</td><td>Includes %Dense and %Sparse header files (the whole Eigen library)</td></tr>
 </table>
@@ -55,7 +45,7 @@ All combinations are allowed: you can have a matrix with a fixed number of rows
 Matrix<double, 6, Dynamic>                  // Dynamic number of columns (heap allocation)
 Matrix<double, Dynamic, 2>                  // Dynamic number of rows (heap allocation)
 Matrix<double, Dynamic, Dynamic, RowMajor>  // Fully dynamic, row major (heap allocation)
-Matrix<double, 13, 3>                       // Fully fixed (static allocation)
+Matrix<double, 13, 3>                       // Fully fixed (usually allocated on stack)
 \endcode
 
 In most cases, you can simply use one of the convenience typedefs for \ref matrixtypedefs "matrices" and \ref arraytypedefs "arrays". Some examples:
@@ -89,8 +79,8 @@ MatrixWrapper<Array44f> a1m(a1);
 \endcode
 
 In the rest of this document we will use the following symbols to emphasize the features which are specifics to a given kind of object:
-\li <a name="matrixonly"><a/>\matrixworld linear algebra matrix and vector only
-\li <a name="arrayonly"><a/>\arrayworld array objects only
+\li <a name="matrixonly"></a>\matrixworld linear algebra matrix and vector only
+\li <a name="arrayonly"></a>\arrayworld array objects only
 
 \subsection QuickRef_Basics Basic matrix manipulation
 
@@ -415,19 +405,19 @@ array1 == array2    array1 != array2    array1 == scalar    array1 != scalar
 array1.min(array2)            
 array1.max(array2)            
 array1.abs2()
-array1.abs()                  std::abs(array1)
-array1.sqrt()                 std::sqrt(array1)
-array1.log()                  std::log(array1)
-array1.exp()                  std::exp(array1)
-array1.pow(exponent)          std::pow(array1,exponent)
+array1.abs()                  abs(array1)
+array1.sqrt()                 sqrt(array1)
+array1.log()                  log(array1)
+array1.exp()                  exp(array1)
+array1.pow(exponent)          pow(array1,exponent)
 array1.square()
 array1.cube()
 array1.inverse()
-array1.sin()                  std::sin(array1)
-array1.cos()                  std::cos(array1)
-array1.tan()                  std::tan(array1)
-array1.asin()                 std::asin(array1)
-array1.acos()                 std::acos(array1)
+array1.sin()                  sin(array1)
+array1.cos()                  cos(array1)
+array1.tan()                  tan(array1)
+array1.asin()                 asin(array1)
+array1.acos()                 acos(array1)
 \endcode
 </td></tr>
 </table>
@@ -458,7 +448,7 @@ mat = 2 7 8
 \endcode</td></tr>
 </table>
 
-Special versions of \link DenseBase::minCoeff(Index*,Index*) minCoeff \endlink and \link DenseBase::maxCoeff(Index*,Index*) maxCoeff \endlink:
+Special versions of \link DenseBase::minCoeff(IndexType*,IndexType*) const minCoeff \endlink and \link DenseBase::maxCoeff(IndexType*,IndexType*) const maxCoeff \endlink:
 \code
 int i, j;
 s = vector.minCoeff(&i);        // s == vector[i]
@@ -490,7 +480,7 @@ Read-write access to sub-vectors:
 <tr><td>\code vec1.head(n)\endcode</td><td>\code vec1.head<n>()\endcode</td><td>the first \c n coeffs </td></tr>
 <tr><td>\code vec1.tail(n)\endcode</td><td>\code vec1.tail<n>()\endcode</td><td>the last \c n coeffs </td></tr>
 <tr><td>\code vec1.segment(pos,n)\endcode</td><td>\code vec1.segment<n>(pos)\endcode</td>
-    <td>the \c n coeffs in \n the range [\c pos : \c pos + \c n [</td></tr>
+    <td>the \c n coeffs in the \n range [\c pos : \c pos + \c n - 1]</td></tr>
 <tr class="alt"><td colspan="3">
 
 Read-write access to sub-matrices:</td></tr>
diff --git a/doc/C00_QuickStartGuide.dox b/doc/QuickStartGuide.dox
index 8534cb0c3..ea32c3b3d 100644
--- a/doc/C00_QuickStartGuide.dox
+++ b/doc/QuickStartGuide.dox
@@ -1,7 +1,8 @@
 namespace Eigen {
 
 /** \page GettingStarted Getting started
-    \ingroup Tutorial
+
+\eigenAutoToc
 
 This is a very short guide on how to get started with Eigen. It has a dual purpose. It serves as a minimal introduction to the Eigen library for people who want to start coding as soon as possible. You can also read this page as the first part of the Tutorial, which explains the library in more detail; in this case you will continue with \ref TutorialMatrixClass.
 
diff --git a/doc/SparseLinearSystems.dox b/doc/SparseLinearSystems.dox
new file mode 100644
index 000000000..c00be10d3
--- /dev/null
+++ b/doc/SparseLinearSystems.dox
@@ -0,0 +1,183 @@
+namespace Eigen {
+/** \eigenManualPage TopicSparseSystems Solving Sparse Linear Systems
+In Eigen, there are several methods available to solve linear systems when the coefficient matrix is sparse. Because of the special representation of this class of matrices, special care should be taken in order to get a good performance. See \ref TutorialSparse for a detailed introduction about sparse matrices in Eigen. This page lists the sparse solvers available in Eigen. The main steps that are common to all these linear solvers are introduced as well. Depending on the properties of the matrix, the desired accuracy, the end-user is able to tune those steps in order to improve the performance of its code. Note that it is not required to know deeply what's hiding behind these steps: the last section presents a benchmark routine that can be easily used to get an insight on the performance of all the available solvers. 
+
+\eigenAutoToc
+
+\section TutorialSparseDirectSolvers Sparse solvers
+
+%Eigen currently provides a limited set of built-in solvers, as well as wrappers to external solver libraries.
+They are summarized in the following table:
+
+<table class="manual">
+<tr><th>Class</th><th>Module</th><th>Solver kind</th><th>Matrix kind</th><th>Features related to performance</th>
+    <th>Dependencies,License</th><th class="width20em"><p>Notes</p></th></tr>
+<tr><td>SimplicialLLT    </td><td>\link SparseCholesky_Module SparseCholesky \endlink</td><td>Direct LLt factorization</td><td>SPD</td><td>Fill-in reducing</td>
+    <td>built-in, LGPL</td>
+    <td>SimplicialLDLT is often preferable</td></tr>
+<tr><td>SimplicialLDLT   </td><td>\link SparseCholesky_Module SparseCholesky \endlink</td><td>Direct LDLt factorization</td><td>SPD</td><td>Fill-in reducing</td>
+    <td>built-in, LGPL</td>
+    <td>Recommended for very sparse and not too large problems (e.g., 2D Poisson eq.)</td></tr>
+<tr><td>ConjugateGradient</td><td>\link IterativeLinearSolvers_Module IterativeLinearSolvers \endlink</td><td>Classic iterative CG</td><td>SPD</td><td>Preconditionning</td>
+    <td>built-in, MPL2</td>
+    <td>Recommended for large symmetric problems (e.g., 3D Poisson eq.)</td></tr>
+<tr><td>BiCGSTAB</td><td>\link IterativeLinearSolvers_Module IterativeLinearSolvers \endlink</td><td>Iterative stabilized bi-conjugate gradient</td><td>Square</td><td>Preconditionning</td>
+    <td>built-in, MPL2</td>
+    <td>To speedup the convergence, try it with the \ref IncompleteLUT preconditioner.</td></tr>
+<tr><td>SparseLU</td> <td>\link SparseLU_Module SparseLU \endlink </td> <td>LU factorization </td>
+    <td>Square </td><td>Fill-in reducing, Leverage fast dense algebra</td>
+    <td> built-in, MPL2</td> <td>optimized for small and large problems with irregular patterns </td></tr>
+<tr><td>SparseQR</td> <td>\link SparseQR_Module SparseQR \endlink</td> <td> QR factorization</td>
+    <td>Any, rectangular</td><td> Fill-in reducing</td>
+    <td>built-in, MPL2</td><td>recommended for least-square problems, has a basic rank-revealing feature</td></tr>
+<tr> <th colspan="7"> Wrappers to external solvers </th></tr>
+<tr><td>PastixLLT \n PastixLDLT \n PastixLU</td><td>\link PaStiXSupport_Module PaStiXSupport \endlink</td><td>Direct LLt, LDLt, LU factorizations</td><td>SPD \n SPD \n Square</td><td>Fill-in reducing, Leverage fast dense algebra, Multithreading</td>
+    <td>Requires the <a href="http://pastix.gforge.inria.fr">PaStiX</a> package, \b CeCILL-C </td>
+    <td>optimized for tough problems and symmetric patterns</td></tr>
+<tr><td>CholmodSupernodalLLT</td><td>\link CholmodSupport_Module CholmodSupport \endlink</td><td>Direct LLt factorization</td><td>SPD</td><td>Fill-in reducing, Leverage fast dense algebra</td>
+    <td>Requires the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">SuiteSparse</a> package, \b GPL </td>
+    <td></td></tr>
+<tr><td>UmfPackLU</td><td>\link UmfPackSupport_Module UmfPackSupport \endlink</td><td>Direct LU factorization</td><td>Square</td><td>Fill-in reducing, Leverage fast dense algebra</td>
+    <td>Requires the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">SuiteSparse</a> package, \b GPL </td>
+    <td></td></tr>
+<tr><td>SuperLU</td><td>\link SuperLUSupport_Module SuperLUSupport \endlink</td><td>Direct LU factorization</td><td>Square</td><td>Fill-in reducing, Leverage fast dense algebra</td>
+    <td>Requires the <a href="http://crd-legacy.lbl.gov/~xiaoye/SuperLU/">SuperLU</a> library, (BSD-like)</td>
+    <td></td></tr>
+<tr><td>SPQR</td><td>\link SPQRSupport_Module SPQRSupport \endlink  </td> <td> QR factorization </td> 
+    <td> Any, rectangular</td><td>fill-in reducing, multithreaded, fast dense algebra</td>
+    <td> requires the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">SuiteSparse</a> package, \b GPL </td><td>recommended for linear least-squares problems, has a rank-revealing feature</tr>
+</table>
+
+Here \c SPD means symmetric positive definite.
+
+All these solvers follow the same general concept.
+Here is a typical and general example:
+\code
+#include <Eigen/RequiredModuleName>
+// ...
+SparseMatrix<double> A;
+// fill A
+VectorXd b, x;
+// fill b
+// solve Ax = b
+SolverClassName<SparseMatrix<double> > solver;
+solver.compute(A);
+if(solver.info()!=Success) {
+  // decomposition failed
+  return;
+}
+x = solver.solve(b);
+if(solver.info()!=Success) {
+  // solving failed
+  return;
+}
+// solve for another right hand side:
+x1 = solver.solve(b1);
+\endcode
+
+For \c SPD solvers, a second optional template argument allows to specify which triangular part have to be used, e.g.:
+
+\code
+#include <Eigen/IterativeLinearSolvers>
+
+ConjugateGradient<SparseMatrix<double>, Eigen::Upper> solver;
+x = solver.compute(A).solve(b);
+\endcode
+In the above example, only the upper triangular part of the input matrix A is considered for solving. The opposite triangle might either be empty or contain arbitrary values.
+
+In the case where multiple problems with the same sparsity pattern have to be solved, then the "compute" step can be decomposed as follow:
+\code
+SolverClassName<SparseMatrix<double> > solver;
+solver.analyzePattern(A);   // for this step the numerical values of A are not used
+solver.factorize(A);
+x1 = solver.solve(b1);
+x2 = solver.solve(b2);
+...
+A = ...;                    // modify the values of the nonzeros of A, the nonzeros pattern must stay unchanged
+solver.factorize(A);
+x1 = solver.solve(b1);
+x2 = solver.solve(b2);
+...
+\endcode
+The compute() method is equivalent to calling both analyzePattern() and factorize().
+
+Finally, each solver provides some specific features, such as determinant, access to the factors, controls of the iterations, and so on.
+More details are availble in the documentations of the respective classes.
+
+\section TheSparseCompute The Compute Step
+In the compute() function, the matrix is generally factorized: LLT for self-adjoint matrices, LDLT for general hermitian matrices, LU for non hermitian matrices and QR for rectangular matrices. These are the results of using direct solvers. For this class of solvers precisely, the compute step is further subdivided into analyzePattern() and factorize(). 
+
+The goal of analyzePattern() is to reorder the nonzero elements of the matrix, such that the factorization step creates less fill-in. This step exploits only the structure of the matrix. Hence, the results of this step can be used for other linear systems where the matrix has the same structure. Note however that sometimes, some external solvers (like SuperLU) require that the values of the matrix are set in this step, for instance to equilibrate the rows and columns of the matrix. In this situation, the results of this step should not be used with other matrices.
+
+Eigen provides a limited set of methods to reorder the matrix in this step, either built-in (COLAMD, AMD) or external (METIS). These methods are set in template parameter list of the solver :
+\code
+DirectSolverClassName<SparseMatrix<double>, OrderingMethod<IndexType> > solver;
+\endcode 
+
+See the \link OrderingMethods_Module OrderingMethods module \endlink for the list of available methods and the associated options. 
+
+In factorize(), the factors of the coefficient matrix are computed. This step should be called each time the values of the matrix change. However, the structural pattern of the matrix should not change between multiple calls. 
+
+For iterative solvers, the compute step is used to eventually setup a preconditioner. For instance, with the ILUT preconditioner, the incomplete factors L and U are computed in this step. Remember that, basically, the goal of the preconditioner is to speedup the convergence of an iterative method by solving a modified linear system where the coefficient matrix has more clustered eigenvalues. For real problems, an iterative solver should always be used with a preconditioner. In Eigen, a preconditioner is  selected by simply adding it as a template parameter to the iterative solver object. 
+\code
+IterativeSolverClassName<SparseMatrix<double>, PreconditionerName<SparseMatrix<double> > solver; 
+\endcode
+The member function preconditioner() returns a read-write reference to the preconditioner 
+ to directly interact with it. See the \link IterativeLinearSolvers_Module Iterative solvers module \endlink and the documentation of each class for the list of available methods.
+
+\section TheSparseSolve The Solve step
+The solve() function computes the solution of the linear systems with one or many right hand sides.
+\code
+X = solver.solve(B);
+\endcode 
+Here, B  can be a vector or a matrix where the columns form the different right hand sides. The solve() function can be called several times as well, for instance when all the right hand sides are not available at once. 
+\code
+x1 = solver.solve(b1);
+// Get the second right hand side b2
+x2 = solver.solve(b2); 
+//  ...
+\endcode
+For direct methods, the solution are computed at the machine precision. Sometimes, the solution need not be too accurate. In this case, the iterative methods are more suitable and the desired accuracy can be set before the solve step using \b setTolerance(). For all the available functions, please, refer to the documentation of the \link IterativeLinearSolvers_Module Iterative solvers module \endlink. 
+
+\section BenchmarkRoutine
+Most of the time, all you need is to know how much time it will take to qolve your system, and hopefully, what is the most suitable solver. In Eigen, we provide a benchmark routine that can be used for this purpose. It is very easy to use. In the build directory, navigate to bench/spbench and compile the routine by typing \b make \e spbenchsolver. Run it with --help option to get the list of all available options. Basically, the matrices to test should be in <a href="http://math.nist.gov/MatrixMarket/formats.html">MatrixMarket Coordinate format</a>, and the routine returns the statistics from all available solvers in Eigen. 
+
+The following table gives an example of XML statistics from several Eigen built-in and external solvers. 
+<TABLE border="1">
+ <TR><TH>Matrix <TH> N <TH> NNZ <TH>  <TH > UMFPACK <TH > SUPERLU <TH > PASTIX LU <TH >BiCGSTAB <TH > BiCGSTAB+ILUT <TH >GMRES+ILUT<TH > LDLT <TH> CHOLMOD LDLT <TH > PASTIX LDLT <TH > LLT <TH > CHOLMOD SP LLT <TH > CHOLMOD LLT <TH > PASTIX LLT <TH> CG</TR>
+<TR><TH rowspan="4">vector_graphics <TD rowspan="4"> 12855 <TD rowspan="4"> 72069 <TH>Compute Time <TD>0.0254549<TD>0.0215677<TD>0.0701827<TD>0.000153388<TD>0.0140107<TD>0.0153709<TD>0.0101601<TD style="background-color:red">0.00930502<TD>0.0649689
+<TR><TH>Solve Time <TD>0.00337835<TD>0.000951826<TD>0.00484373<TD>0.0374886<TD>0.0046445<TD>0.00847754<TD>0.000541813<TD style="background-color:red">0.000293696<TD>0.00485376
+<TR><TH>Total Time <TD>0.0288333<TD>0.0225195<TD>0.0750265<TD>0.037642<TD>0.0186552<TD>0.0238484<TD>0.0107019<TD style="background-color:red">0.00959871<TD>0.0698227
+<TR><TH>Error(Iter) <TD> 1.299e-16 <TD> 2.04207e-16 <TD> 4.83393e-15 <TD> 3.94856e-11 (80)  <TD> 1.03861e-12 (3)  <TD> 5.81088e-14 (6)  <TD> 1.97578e-16 <TD> 1.83927e-16 <TD> 4.24115e-15
+<TR><TH rowspan="4">poisson_SPD <TD rowspan="4"> 19788 <TD rowspan="4"> 308232 <TH>Compute Time <TD>0.425026<TD>1.82378<TD>0.617367<TD>0.000478921<TD>1.34001<TD>1.33471<TD>0.796419<TD>0.857573<TD>0.473007<TD>0.814826<TD style="background-color:red">0.184719<TD>0.861555<TD>0.470559<TD>0.000458188
+<TR><TH>Solve Time <TD>0.0280053<TD>0.0194402<TD>0.0268747<TD>0.249437<TD>0.0548444<TD>0.0926991<TD>0.00850204<TD>0.0053171<TD>0.0258932<TD>0.00874603<TD style="background-color:red">0.00578155<TD>0.00530361<TD>0.0248942<TD>0.239093
+<TR><TH>Total Time <TD>0.453031<TD>1.84322<TD>0.644241<TD>0.249916<TD>1.39486<TD>1.42741<TD>0.804921<TD>0.862891<TD>0.4989<TD>0.823572<TD style="background-color:red">0.190501<TD>0.866859<TD>0.495453<TD>0.239551
+<TR><TH>Error(Iter) <TD> 4.67146e-16 <TD> 1.068e-15 <TD> 1.3397e-15 <TD> 6.29233e-11 (201)  <TD> 3.68527e-11 (6)  <TD> 3.3168e-15 (16)  <TD> 1.86376e-15 <TD> 1.31518e-16 <TD> 1.42593e-15 <TD> 3.45361e-15 <TD> 3.14575e-16 <TD> 2.21723e-15 <TD> 7.21058e-16 <TD> 9.06435e-12 (261) 
+<TR><TH rowspan="4">sherman2 <TD rowspan="4"> 1080 <TD rowspan="4"> 23094 <TH>Compute Time <TD style="background-color:red">0.00631754<TD>0.015052<TD>0.0247514 <TD> -<TD>0.0214425<TD>0.0217988
+<TR><TH>Solve Time <TD style="background-color:red">0.000478424<TD>0.000337998<TD>0.0010291 <TD> -<TD>0.00243152<TD>0.00246152
+<TR><TH>Total Time <TD style="background-color:red">0.00679597<TD>0.01539<TD>0.0257805 <TD> -<TD>0.023874<TD>0.0242603
+<TR><TH>Error(Iter) <TD> 1.83099e-15 <TD> 8.19351e-15 <TD> 2.625e-14 <TD> 1.3678e+69 (1080)  <TD> 4.1911e-12 (7)  <TD> 5.0299e-13 (12) 
+<TR><TH rowspan="4">bcsstk01_SPD <TD rowspan="4"> 48 <TD rowspan="4"> 400 <TH>Compute Time <TD>0.000169079<TD>0.00010789<TD>0.000572538<TD>1.425e-06<TD>9.1612e-05<TD>8.3985e-05<TD style="background-color:red">5.6489e-05<TD>7.0913e-05<TD>0.000468251<TD>5.7389e-05<TD>8.0212e-05<TD>5.8394e-05<TD>0.000463017<TD>1.333e-06
+<TR><TH>Solve Time <TD>1.2288e-05<TD>1.1124e-05<TD>0.000286387<TD>8.5896e-05<TD>1.6381e-05<TD>1.6984e-05<TD style="background-color:red">3.095e-06<TD>4.115e-06<TD>0.000325438<TD>3.504e-06<TD>7.369e-06<TD>3.454e-06<TD>0.000294095<TD>6.0516e-05
+<TR><TH>Total Time <TD>0.000181367<TD>0.000119014<TD>0.000858925<TD>8.7321e-05<TD>0.000107993<TD>0.000100969<TD style="background-color:red">5.9584e-05<TD>7.5028e-05<TD>0.000793689<TD>6.0893e-05<TD>8.7581e-05<TD>6.1848e-05<TD>0.000757112<TD>6.1849e-05
+<TR><TH>Error(Iter) <TD> 1.03474e-16 <TD> 2.23046e-16 <TD> 2.01273e-16 <TD> 4.87455e-07 (48)  <TD> 1.03553e-16 (2)  <TD> 3.55965e-16 (2)  <TD> 2.48189e-16 <TD> 1.88808e-16 <TD> 1.97976e-16 <TD> 2.37248e-16 <TD> 1.82701e-16 <TD> 2.71474e-16 <TD> 2.11322e-16 <TD> 3.547e-09 (48) 
+<TR><TH rowspan="4">sherman1 <TD rowspan="4"> 1000 <TD rowspan="4"> 3750 <TH>Compute Time <TD>0.00228805<TD>0.00209231<TD>0.00528268<TD>9.846e-06<TD>0.00163522<TD>0.00162155<TD>0.000789259<TD style="background-color:red">0.000804495<TD>0.00438269
+<TR><TH>Solve Time <TD>0.000213788<TD>9.7983e-05<TD>0.000938831<TD>0.00629835<TD>0.000361764<TD>0.00078794<TD>4.3989e-05<TD style="background-color:red">2.5331e-05<TD>0.000917166
+<TR><TH>Total Time <TD>0.00250184<TD>0.00219029<TD>0.00622151<TD>0.0063082<TD>0.00199698<TD>0.00240949<TD>0.000833248<TD style="background-color:red">0.000829826<TD>0.00529986
+<TR><TH>Error(Iter) <TD> 1.16839e-16 <TD> 2.25968e-16 <TD> 2.59116e-16 <TD> 3.76779e-11 (248)  <TD> 4.13343e-11 (4)  <TD> 2.22347e-14 (10)  <TD> 2.05861e-16 <TD> 1.83555e-16 <TD> 1.02917e-15
+<TR><TH rowspan="4">young1c <TD rowspan="4"> 841 <TD rowspan="4"> 4089 <TH>Compute Time <TD>0.00235843<TD style="background-color:red">0.00217228<TD>0.00568075<TD>1.2735e-05<TD>0.00264866<TD>0.00258236
+<TR><TH>Solve Time <TD>0.000329599<TD style="background-color:red">0.000168634<TD>0.00080118<TD>0.0534738<TD>0.00187193<TD>0.00450211
+<TR><TH>Total Time <TD>0.00268803<TD style="background-color:red">0.00234091<TD>0.00648193<TD>0.0534865<TD>0.00452059<TD>0.00708447
+<TR><TH>Error(Iter) <TD> 1.27029e-16 <TD> 2.81321e-16 <TD> 5.0492e-15 <TD> 8.0507e-11 (706)  <TD> 3.00447e-12 (8)  <TD> 1.46532e-12 (16) 
+<TR><TH rowspan="4">mhd1280b <TD rowspan="4"> 1280 <TD rowspan="4"> 22778 <TH>Compute Time <TD>0.00234898<TD>0.00207079<TD>0.00570918<TD>2.5976e-05<TD>0.00302563<TD>0.00298036<TD>0.00144525<TD style="background-color:red">0.000919922<TD>0.00426444
+<TR><TH>Solve Time <TD>0.00103392<TD>0.000211911<TD>0.00105<TD>0.0110432<TD>0.000628287<TD>0.00392089<TD>0.000138303<TD style="background-color:red">6.2446e-05<TD>0.00097564
+<TR><TH>Total Time <TD>0.0033829<TD>0.0022827<TD>0.00675918<TD>0.0110692<TD>0.00365392<TD>0.00690124<TD>0.00158355<TD style="background-color:red">0.000982368<TD>0.00524008
+<TR><TH>Error(Iter) <TD> 1.32953e-16 <TD> 3.08646e-16 <TD> 6.734e-16 <TD> 8.83132e-11 (40)  <TD> 1.51153e-16 (1)  <TD> 6.08556e-16 (8)  <TD> 1.89264e-16 <TD> 1.97477e-16 <TD> 6.68126e-09
+<TR><TH rowspan="4">crashbasis <TD rowspan="4"> 160000 <TD rowspan="4"> 1750416 <TH>Compute Time <TD>3.2019<TD>5.7892<TD>15.7573<TD style="background-color:red">0.00383515<TD>3.1006<TD>3.09921
+<TR><TH>Solve Time <TD>0.261915<TD>0.106225<TD>0.402141<TD style="background-color:red">1.49089<TD>0.24888<TD>0.443673
+<TR><TH>Total Time <TD>3.46381<TD>5.89542<TD>16.1594<TD style="background-color:red">1.49473<TD>3.34948<TD>3.54288
+<TR><TH>Error(Iter) <TD> 1.76348e-16 <TD> 4.58395e-16 <TD> 1.67982e-14 <TD> 8.64144e-11 (61)  <TD> 8.5996e-12 (2)  <TD> 6.04042e-14 (5) 
+
+</TABLE>
+*/
+}
diff --git a/doc/SparseQuickReference.dox b/doc/SparseQuickReference.dox
index 7d6eb0fa9..4a33d0cc9 100644
--- a/doc/SparseQuickReference.dox
+++ b/doc/SparseQuickReference.dox
@@ -1,74 +1,87 @@
 namespace Eigen {
-/** \page SparseQuickRefPage Quick reference guide for sparse matrices
-
-\b Table \b of \b contents
-  - \ref Constructors
-  - \ref SparseMatrixInsertion
-  - \ref SparseBasicInfos
-  - \ref SparseBasicOps
-  - \ref SparseInterops
-  - \ref sparsepermutation
-  - \ref sparsesubmatrices
-  - \ref sparseselfadjointview
-\n 
+/** \eigenManualPage SparseQuickRefPage Quick reference guide for sparse matrices
+\eigenAutoToc
 
 <hr>
 
-In this page, we give a quick summary of the main operations available for sparse matrices in the class SparseMatrix. First, it is recommended to read first the introductory tutorial at \ref TutorialSparse. The important point to have in mind when working on sparse matrices is how they are stored : 
-i.e either row major or column major. The default is column major. Most arithmetic operations on sparse matrices will assert that they have the same storage order. Moreover, when interacting with external libraries that are not yet supported by Eigen, it is important to know how to send the required matrix pointers. 
-
-\section Constructors Constructors and assignments
-SparseMatrix is the core class to build and manipulate sparse matrices in Eigen. It takes as template parameters the Scalar type and the storage order, either RowMajor or ColumnMajor. The default is ColumnMajor.
+In this page, we give a quick summary of the main operations available for sparse matrices in the class SparseMatrix. First, it is recommended to read  the introductory tutorial at \ref TutorialSparse. The important point to have in mind when working on sparse matrices is how they are stored : 
+i.e either row major or column major. The default is column major. Most arithmetic operations on sparse matrices will assert that they have the same storage order. 
 
+\section SparseMatrixInit Sparse Matrix Initialization
+<table class="manual">
+<tr><th> Category </th> <th> Operations</th> <th>Notes</th></tr>
+<tr><td>Constructor</td>
+<td>
 \code
-  SparseMatrix<double> sm1(1000,1000);              // 1000x1000 compressed sparse matrix of double. 
-  SparseMatrix<std::complex<double>,RowMajor> sm2; // Compressed row major matrix of complex double.
+  SparseMatrix<double> sm1(1000,1000); 
+  SparseMatrix<std::complex<double>,RowMajor> sm2;
 \endcode
-The copy constructor and assignment can be used to convert matrices from a storage order to another
+</td> <td> Default is ColMajor</td> </tr>
+<tr class="alt">
+<td> Resize/Reserve</td>
+<td> 
+ \code
+    sm1.resize(m,n);      //Change sm1 to a m x n matrix. 
+    sm1.reserve(nnz);     // Allocate room for nnz nonzeros elements.   
+  \endcode 
+</td>
+<td> Note that when calling reserve(), it is not required that nnz is the exact number of nonzero elements in the final matrix. However, an exact estimation will avoid multiple reallocations during the insertion phase. </td>
+</tr>
+<tr> 
+<td> Assignment </td>
+<td> 
 \code 
   SparseMatrix<double,Colmajor> sm1;
-  // Eventually fill the matrix sm1 ...
-  SparseMatrix<double,Rowmajor> sm2(sm1), sm3;         // Initialize sm2 with sm1.
-  sm3 = sm1; // Assignment and evaluations modify the storage order.
+ // Initialize sm2 with sm1.
+  SparseMatrix<double,Rowmajor> sm2(sm1), sm3;        
+  // Assignment and evaluations modify the storage order.
+  sm3 = sm1; 
  \endcode
-
-\section SparseMatrixInsertion  Allocating and inserting values
-resize() and reserve() are used to set the size and allocate space for nonzero elements
- \code
-    sm1.resize(m,n);      //Change sm to a mxn matrix. 
-    sm1.reserve(nnz);     // Allocate  room for nnz nonzeros elements.   
-  \endcode 
-Note that when calling reserve(), it is not required that nnz is the exact number of nonzero elements in the final matrix. However, an exact estimation will avoid multiple reallocations during the insertion phase. 
-
-Insertions of values in the sparse matrix can be done directly by looping over nonzero elements and use the insert() function
+</td>
+<td> The copy constructor can be used to convert from a storage order to another</td>
+</tr>
+<tr class="alt">
+<td> Element-wise Insertion</td>
+<td>
 \code 
-// Direct insertion of the value v_ij; 
-  sm1.insert(i, j) = v_ij;   // It is assumed that v_ij does not already exist in the matrix. 
-\endcode
+// Insert a new element; 
+ sm1.insert(i, j) = v_ij;  
 
-After insertion, a value at (i,j) can be modified using coeffRef()
-\code
-  // Update the value v_ij
-  sm1.coeffRef(i,j) = v_ij;
-  sm1.coeffRef(i,j) += v_ij;
-  sm1.coeffRef(i,j) -= v_ij;
-  ...
+// Update the value v_ij
+ sm1.coeffRef(i,j) = v_ij;
+ sm1.coeffRef(i,j) += v_ij;
+ sm1.coeffRef(i,j) -= v_ij;
 \endcode
-
-The recommended way to insert values is to build a list of triplets (row, col, val) and then call setFromTriplets(). 
+</td>
+<td> insert() assumes that the element does not already exist; otherwise, use coeffRef()</td>
+</tr>
+<tr> 
+<td> Batch insertion</td>
+<td>
 \code
+  std::vector< Eigen::Triplet<double> > tripletList;
+  tripletList.reserve(estimation_of_entries);
+  // -- Fill tripletList with nonzero elements...
   sm1.setFromTriplets(TripletList.begin(), TripletList.end());
 \endcode
-A complete example is available at \ref TutorialSparseFilling.
-
-The following functions can be used to set constant or random values in the matrix.
+</td>
+<td>A complete example is available at \link TutorialSparseFilling Triplet Insertion \endlink.</td>
+</tr>
+<tr class="alt"> 
+<td> Constant or Random Insertion</td>
+<td>
 \code
-  sm1.setZero(); // Reset the matrix with zero elements
-  ...
+sm1.setZero(); // Set the matrix with zero elements
+sm1.setConstant(val); //Replace all the nonzero values with val
 \endcode
+</td>
+<td> The matrix sm1 should have been created before ???</td>
+</tr>
+</table>
+
 
 \section SparseBasicInfos Matrix properties
-Beyond the functions rows() and cols() that are used to get the number of rows and columns, there are some useful functions that are available to easily get some informations from the matrix. 
+Beyond the basic functions rows() and cols(), there are some useful functions that are available to easily get some informations from the matrix. 
 <table class="manual">
 <tr>
   <td> \code
@@ -77,16 +90,18 @@ Beyond the functions rows() and cols() that are used to get the number of rows a
   sm1.nonZeros();     // Number of non zero values   
   sm1.outerSize();    // Number of columns (resp. rows) for a column major (resp. row major )
   sm1.innerSize();    // Number of rows (resp. columns) for a row major (resp. column major)
-  sm1.norm();         // (Euclidian ??) norm of the matrix
-  sm1.squaredNorm();  // 
+  sm1.norm();         // Euclidian norm of the matrix
+  sm1.squaredNorm();  // Squared norm of the matrix
+  sm1.blueNorm();
   sm1.isVector();     // Check if sm1 is a sparse vector or a sparse matrix
+  sm1.isCompressed(); // Check if sm1 is in compressed form
   ...
   \endcode </td>
 </tr>
 </table>
 
 \section SparseBasicOps Arithmetic operations
-It is easy to perform arithmetic operations on sparse matrices provided that the dimensions are adequate and that the matrices have the same storage order. Note that the evaluation can always be done in a matrix with a different storage order. 
+It is easy to perform arithmetic operations on sparse matrices provided that the dimensions are adequate and that the matrices have the same storage order. Note that the evaluation can always be done in a matrix with a different storage order. In the following, \b sm denotes a sparse matrix, \b dm a dense matrix and \b dv a dense vector.
 <table class="manual">
 <tr><th> Operations </th> <th> Code </th> <th> Notes </th></tr>
 
@@ -113,7 +128,7 @@ It is easy to perform arithmetic operations on sparse matrices provided that the
 </tr>
 
 <tr>
-  <td> Product </td>
+  <td> %Sparse %Product </td>
   <td> \code
   sm3 = sm1 * sm2;
   dm2 = sm1 * dm1;
@@ -133,7 +148,20 @@ It is easy to perform arithmetic operations on sparse matrices provided that the
   Note that the transposition change the storage order. There is no support for transposeInPlace().
   </td>
 </tr> 
-
+<tr>
+<td> Permutation </td>
+<td> 
+\code 
+perm.indices(); // Reference to the vector of indices
+sm1.twistedBy(perm); // Permute rows and columns
+sm2 = sm1 * perm; //Permute the columns
+sm2 = perm * sm1; // Permute the columns
+\endcode 
+</td>
+<td> 
+
+</td>
+</tr>
 <tr>
   <td>
   Component-wise ops
@@ -152,47 +180,70 @@ It is easy to perform arithmetic operations on sparse matrices provided that the
 </tr>
 </table>
 
-
-\section SparseInterops Low-level storage
-There are a set of low-levels functions to get the standard compressed storage pointers. The matrix should be in compressed mode which can be checked by calling isCompressed(); makeCompressed() should do the job otherwise. 
+\section sparseotherops Other supported operations
+<table class="manual">
+<tr><th>Operations</th> <th> Code </th> <th> Notes</th> </tr>
+<tr>
+<td>Sub-matrices</td> 
+<td> 
+\code 
+  sm1.block(startRow, startCol, rows, cols); 
+  sm1.block(startRow, startCol); 
+  sm1.topLeftCorner(rows, cols); 
+  sm1.topRightCorner(rows, cols);
+  sm1.bottomLeftCorner( rows, cols);
+  sm1.bottomRightCorner( rows, cols);
+  \endcode
+</td> <td>  </td>
+</tr>
+<tr> 
+<td> Range </td>
+<td> 
+\code 
+  sm1.innerVector(outer); 
+  sm1.innerVectors(start, size);
+  sm1.leftCols(size);
+  sm2.rightCols(size);
+  sm1.middleRows(start, numRows);
+  sm1.middleCols(start, numCols);
+  sm1.col(j);
+\endcode
+</td>
+<td>A inner vector is either a row (for row-major) or a column (for column-major). As stated earlier, the evaluation can be done in a matrix with different storage order </td>
+</tr>
+<tr>
+<td> Triangular and selfadjoint views</td>
+<td> 
 \code
-  // Scalar pointer to the values of the matrix, size nnz
-  sm1.valuePtr();  
-  // Index pointer to get the row indices (resp. column indices) for column major (resp. row major) matrix, size nnz
-  sm1.innerIndexPtr();
-  // Index pointer to the beginning of each row (resp. column) in valuePtr() and innerIndexPtr() for column major (row major). The size is outersize()+1; 
-  sm1.outerIndexPtr();  
+  sm2 = sm1.triangularview<Lower>();
+  sm2 = sm1.selfadjointview<Lower>();
 \endcode
-These pointers can therefore be easily used to send the matrix to some external libraries/solvers that are not yet supported by Eigen.
-
-\section sparsepermutation Permutations, submatrices and Selfadjoint Views
-In many cases, it is necessary to reorder the rows and/or the columns of the sparse matrix for several purposes : fill-in reducing during matrix decomposition, better data locality for sparse matrix-vector products... The class PermutationMatrix is available to this end. 
- \code
-  PermutationMatrix<Dynamic, Dynamic, int> perm;
-  // Reserve and fill the values of perm; 
-  perm.inverse(n); // Compute eventually the inverse permutation
-  sm1.twistedBy(perm) //Apply the permutation on rows and columns 
-  sm2 = sm1 * perm; // ??? Apply the permutation on columns ???; 
-  sm2 = perm * sm1; // ??? Apply the permutation on rows ???; 
-  \endcode
-
-\section sparsesubmatrices Sub-matrices
-The following functions are useful to extract a block of rows (resp. columns) from a row-major (resp. column major) sparse matrix. Note that because of the particular storage, it is not ?? efficient ?? to extract a submatrix comprising a certain number of subrows and subcolumns.
- \code
-  sm1.innerVector(outer); // Returns the outer -th column (resp. row) of the matrix if sm is col-major (resp. row-major)
-  sm1.innerVectors(outer); // Returns the outer -th column (resp. row) of the matrix if mat is col-major (resp. row-major)
-  sm1.middleRows(start, numRows); // For row major matrices, get a range of numRows rows
-  sm1.middleCols(start, numCols); // For column major matrices, get a range of numCols cols
- \endcode 
- Examples : 
-
-\section sparseselfadjointview Sparse triangular and selfadjoint Views
- \code
-  sm2 = sm1.triangularview<Lower>(); // Get the lower triangular part of the matrix. 
-  dv2 = sm1.triangularView<Upper>().solve(dv1); // Solve the linear system with the uppper triangular part. 
-  sm2 = sm1.selfadjointview<Lower>(); // Build a selfadjoint matrix from the lower part of sm1. 
-  \endcode
-
-
+</td>
+<td> Several combination between triangular views and blocks views are possible
+\code 
+  \endcode </td>
+</tr>
+<tr> 
+<td>Triangular solve </td>
+<td> 
+\code 
+ dv2 = sm1.triangularView<Upper>().solve(dv1);
+ dv2 = sm1.topLeftCorner(size, size).triangularView<Lower>().solve(dv1);
+\endcode 
+</td>
+<td> For general sparse solve, Use any suitable module described at \ref TopicSparseSystems </td>
+</tr>
+<tr>
+<td> Low-level API</td>
+<td>
+\code
+sm1.valuePtr(); // Pointer to the values
+sm1.innerIndextr(); // Pointer to the indices.
+sm1.outerIndexPtr(); //Pointer to the beginning of each inner vector
+\endcode
+</td>
+<td> If the matrix is not in compressed form, makeCompressed() should be called before. Note that these functions are mostly provided for interoperability purposes with external libraries. A better access to the values of the matrix is done by using the InnerIterator class as described in \link TutorialSparse the Tutorial Sparse \endlink section</td>
+</tr>
+</table>
 */
 }
diff --git a/doc/D01_StlContainers.dox b/doc/StlContainers.dox
index b5dbf0698..d8d0d529c 100644
--- a/doc/D01_StlContainers.dox
+++ b/doc/StlContainers.dox
@@ -1,11 +1,8 @@
 namespace Eigen {
 
-/** \page TopicStlContainers Using STL Containers with Eigen
+/** \eigenManualPage TopicStlContainers Using STL Containers with Eigen
 
-\b Table \b of \b contents
-  - \ref summary
-  - \ref allocator
-  - \ref vector
+\eigenAutoToc
 
 \section summary Executive summary
 
@@ -38,7 +35,7 @@ The situation with std::vector was even worse (explanation below) so we had to s
 Here is an example:
 \code
 #include<Eigen/StdVector>
-\/* ... *\/
+/* ... */
 std::vector<Eigen::Vector4f,Eigen::aligned_allocator<Eigen::Vector4f> >
 \endcode
 
@@ -52,7 +49,7 @@ the compiler will compile that particular instance with the default std::allocat
 Here is an example:
 \code
 #include<Eigen/StdVector>
-\/* ... *\/
+/* ... */
 EIGEN_DEFINE_STL_VECTOR_SPECIALIZATION(Matrix2d)
 std::vector<Eigen::Vector2d>
 \endcode
diff --git a/doc/I15_StorageOrders.dox b/doc/StorageOrders.dox
index 7418912a6..61645313e 100644
--- a/doc/I15_StorageOrders.dox
+++ b/doc/StorageOrders.dox
@@ -1,14 +1,11 @@
 namespace Eigen {
 
-/** \page TopicStorageOrders Storage orders
+/** \eigenManualPage TopicStorageOrders Storage orders
 
 There are two different storage orders for matrices and two-dimensional arrays: column-major and row-major.
 This page explains these storage orders and how to specify which one should be used.
 
-<b>Table of contents</b>
-  - \ref TopicStorageOrdersIntro
-  - \ref TopicStorageOrdersInEigen
-  - \ref TopicStorageOrdersWhich
+\eigenAutoToc
 
 
 \section TopicStorageOrdersIntro Column-major and row-major storage
diff --git a/doc/D09_StructHavingEigenMembers.dox b/doc/StructHavingEigenMembers.dox
index 51789ca9c..74a8d5217 100644
--- a/doc/D09_StructHavingEigenMembers.dox
+++ b/doc/StructHavingEigenMembers.dox
@@ -1,16 +1,8 @@
 namespace Eigen {
 
-/** \page TopicStructHavingEigenMembers Structures Having Eigen Members
-
-\b Table \b of \b contents
-  - \ref summary
-  - \ref what
-  - \ref how
-  - \ref why
-  - \ref movetotop
-  - \ref bugineigen
-  - \ref conditional
-  - \ref othersolutions
+/** \eigenManualPage TopicStructHavingEigenMembers Structures Having Eigen Members
+
+\eigenAutoToc
 
 \section summary Executive Summary
 
diff --git a/doc/I16_TemplateKeyword.dox b/doc/TemplateKeyword.dox
index 324532310..f4e4f237e 100644
--- a/doc/I16_TemplateKeyword.dox
+++ b/doc/TemplateKeyword.dox
@@ -7,11 +7,7 @@ amongst programmers: to define templates. The other use is more obscure: to spec
 to a template function or a type. This regularly trips up programmers that use the %Eigen library, often
 leading to error messages from the compiler that are difficult to understand.
 
-<b>Table of contents</b>
-  - \ref TopicTemplateKeywordToDefineTemplates
-  - \ref TopicTemplateKeywordExample
-  - \ref TopicTemplateKeywordExplanation
-  - \ref TopicTemplateKeywordResources
+\eigenAutoToc
 
 
 \section TopicTemplateKeywordToDefineTemplates Using the template and typename keywords to define templates
diff --git a/doc/I11_Aliasing.dox b/doc/TopicAliasing.dox
index 7c111991c..c2654aed2 100644
--- a/doc/I11_Aliasing.dox
+++ b/doc/TopicAliasing.dox
@@ -1,19 +1,14 @@
 namespace Eigen {
 
-/** \page TopicAliasing Aliasing
+/** \eigenManualPage TopicAliasing Aliasing
 
-In Eigen, aliasing refers to assignment statement in which the same matrix (or array or vector) appears on the
+In %Eigen, aliasing refers to assignment statement in which the same matrix (or array or vector) appears on the
 left and on the right of the assignment operators. Statements like <tt>mat = 2 * mat;</tt> or <tt>mat =
 mat.transpose();</tt> exhibit aliasing. The aliasing in the first example is harmless, but the aliasing in the
 second example leads to unexpected results. This page explains what aliasing is, when it is harmful, and what
 to do about it.
 
-<b>Table of contents</b>
-  - \ref TopicAliasingExamples
-  - \ref TopicAliasingSolution
-  - \ref TopicAliasingCwise
-  - \ref TopicAliasingMatrixMult
-  - \ref TopicAliasingSummary
+\eigenAutoToc
 
 
 \section TopicAliasingExamples Examples
@@ -37,7 +32,7 @@ This assignment exhibits aliasing: the coefficient \c mat(1,1) appears both in t
 <tt>mat.bottomRightCorner(2,2)</tt> on the left-hand side of the assignment and the block
 <tt>mat.topLeftCorner(2,2)</tt> on the right-hand side. After the assignment, the (2,2) entry in the bottom
 right corner should have the value of \c mat(1,1) before the assignment, which is 5. However, the output shows
-that \c mat(2,2) is actually 1. The problem is that Eigen uses lazy evaluation (see 
+that \c mat(2,2) is actually 1. The problem is that %Eigen uses lazy evaluation (see 
 \ref TopicEigenExpressionTemplates) for <tt>mat.topLeftCorner(2,2)</tt>. The result is similar to
 \code
 mat(1,1) = mat(0,0);
@@ -48,10 +43,13 @@ mat(2,2) = mat(1,1);
 Thus, \c mat(2,2) is assigned the \e new value of \c mat(1,1) instead of the old value. The next section
 explains how to solve this problem by calling \link DenseBase::eval() eval()\endlink.
 
-Note that if \c mat were a bigger, then the blocks would not overlap, and there would be no aliasing
-problem. This means that in general aliasing cannot be detected at compile time. However, Eigen does detect
-some instances of aliasing, albeit at run time.  The following example exhibiting aliasing was mentioned in
-\ref TutorialMatrixArithmetic :
+Aliasing occurs more naturally when trying to shrink a matrix. For example, the expressions <tt>vec =
+vec.head(n)</tt> and <tt>mat = mat.block(i,j,r,c)</tt> exhibit aliasing.
+
+In general, aliasing cannot be detected at compile time: if \c mat in the first example were a bit bigger,
+then the blocks would not overlap, and there would be no aliasing problem. However, %Eigen does detect some
+instances of aliasing, albeit at run time.  The following example exhibiting aliasing was mentioned in \ref
+TutorialMatrixArithmetic :
 
 <table class="example">
 <tr><th>Example</th><th>Output</th></tr>
@@ -62,24 +60,24 @@ some instances of aliasing, albeit at run time.  The following example exhibitin
 \verbinclude tut_arithmetic_transpose_aliasing.out
 </td></tr></table>
 
-Again, the output shows the aliasing issue. However, by default Eigen uses a run-time assertion to detect this
+Again, the output shows the aliasing issue. However, by default %Eigen uses a run-time assertion to detect this
 and exits with a message like
 
 \verbatim
 void Eigen::DenseBase<Derived>::checkTransposeAliasing(const OtherDerived&) const 
 [with OtherDerived = Eigen::Transpose<Eigen::Matrix<int, 2, 2, 0, 2, 2> >, Derived = Eigen::Matrix<int, 2, 2, 0, 2, 2>]: 
 Assertion `(!internal::check_transpose_aliasing_selector<Scalar,internal::blas_traits<Derived>::IsTransposed,OtherDerived>::run(internal::extract_data(derived()), other)) 
-&& "aliasing detected during tranposition, use transposeInPlace() or evaluate the rhs into a temporary using .eval()"' failed.
+&& "aliasing detected during transposition, use transposeInPlace() or evaluate the rhs into a temporary using .eval()"' failed.
 \endverbatim
 
-The user can turn Eigen's run-time assertions like the one to detect this aliasing problem off by defining the
+The user can turn %Eigen's run-time assertions like the one to detect this aliasing problem off by defining the
 EIGEN_NO_DEBUG macro, and the above program was compiled with this macro turned off in order to illustrate the
-aliasing problem. See \ref TopicAssertions for more information about Eigen's run-time assertions.
+aliasing problem. See \ref TopicAssertions for more information about %Eigen's run-time assertions.
 
 
 \section TopicAliasingSolution Resolving aliasing issues
 
-If you understand the cause of the aliasing issue, then it is obvious what must happen to solve it: Eigen has
+If you understand the cause of the aliasing issue, then it is obvious what must happen to solve it: %Eigen has
 to evaluate the right-hand side fully into a temporary matrix/array and then assign it to the left-hand
 side. The function \link DenseBase::eval() eval() \endlink does precisely that.
 
@@ -98,7 +96,7 @@ Now, \c mat(2,2) equals 5 after the assignment, as it should be.
 
 The same solution also works for the second example, with the transpose: simply replace the line 
 <tt>a = a.transpose();</tt> with <tt>a = a.transpose().eval();</tt>. However, in this common case there is a
-better solution. Eigen provides the special-purpose function 
+better solution. %Eigen provides the special-purpose function 
 \link DenseBase::transposeInPlace() transposeInPlace() \endlink which replaces a matrix by its transpose. 
 This is shown below:
 
@@ -112,7 +110,7 @@ This is shown below:
 </td></tr></table>
 
 If an xxxInPlace() function is available, then it is best to use it, because it indicates more clearly what you
-are doing. This may also allow Eigen to optimize more aggressively. These are some of the xxxInPlace()
+are doing. This may also allow %Eigen to optimize more aggressively. These are some of the xxxInPlace()
 functions provided: 
 
 <table class="manual">
@@ -125,6 +123,9 @@ functions provided:
 <tr class="alt"> <td> DenseBase::transpose() </td> <td> DenseBase::transposeInPlace() </td> </tr>
 </table>
 
+In the special case where a matrix or vector is shrunk using an expression like <tt>vec = vec.head(n)</tt>,
+you can use \link PlainObjectBase::conservativeResize() conservativeResize() \endlink.
+
 
 \section TopicAliasingCwise Aliasing and component-wise operations
 
@@ -133,8 +134,8 @@ right-hand side of an assignment operator, and it is then often necessary to eva
 explicitly. However, applying component-wise operations (such as matrix addition, scalar multiplication and
 array multiplication) is safe. 
 
-The following example has only component-wise operations. Thus, there is no need for .eval() even though
-the same matrix appears on both sides of the assignments.
+The following example has only component-wise operations. Thus, there is no need for \link DenseBase::eval()
+eval() \endlink even though the same matrix appears on both sides of the assignments.
 
 <table class="example">
 <tr><th>Example</th><th>Output</th></tr>
@@ -152,8 +153,8 @@ not necessary to evaluate the right-hand side explicitly.
 
 \section TopicAliasingMatrixMult Aliasing and matrix multiplication
 
-Matrix multiplication is the only operation in Eigen that assumes aliasing by default. Thus, if \c matA is a
-matrix, then the statement <tt>matA = matA * matA;</tt> is safe. All other operations in Eigen assume that
+Matrix multiplication is the only operation in %Eigen that assumes aliasing by default. Thus, if \c matA is a
+matrix, then the statement <tt>matA = matA * matA;</tt> is safe. All other operations in %Eigen assume that
 there are no aliasing problems, either because the result is assigned to a different matrix or because it is a
 component-wise operation.
 
@@ -166,14 +167,14 @@ component-wise operation.
 \verbinclude TopicAliasing_mult1.out
 </td></tr></table>
 
-However, this comes at a price. When executing the expression <tt>matA = matA * matA</tt>, Eigen evaluates the
-product in a temporary matrix which is assigned to \c matA after the computation. This is fine. But Eigen does
+However, this comes at a price. When executing the expression <tt>matA = matA * matA</tt>, %Eigen evaluates the
+product in a temporary matrix which is assigned to \c matA after the computation. This is fine. But %Eigen does
 the same when the product is assigned to a different matrix (e.g., <tt>matB = matA * matA</tt>). In that case,
 it is more efficient to evaluate the product directly into \c matB instead of evaluating it first into a
 temporary matrix and copying that matrix to \c matB.
 
 The user can indicate with the \link MatrixBase::noalias() noalias()\endlink function that there is no
-aliasing, as follows: <tt>matB.noalias() = matA * matA</tt>. This allows Eigen to evaluate the matrix product
+aliasing, as follows: <tt>matB.noalias() = matA * matA</tt>. This allows %Eigen to evaluate the matrix product
 <tt>matA * matA</tt> directly into \c matB.
 
 <table class="example">
@@ -204,9 +205,9 @@ Aliasing occurs when the same matrix or array coefficients appear both on the le
 an assignment operator.
  - Aliasing is harmless with coefficient-wise computations; this includes scalar multiplication and matrix or
    array addition.
- - When you multiply two matrices, Eigen assumes that aliasing occurs. If you know that there is no aliasing,
+ - When you multiply two matrices, %Eigen assumes that aliasing occurs. If you know that there is no aliasing,
    then you can use \link MatrixBase::noalias() noalias()\endlink.
- - In all other situations, Eigen assumes that there is no aliasing issue and thus gives the wrong result if
+ - In all other situations, %Eigen assumes that there is no aliasing issue and thus gives the wrong result if
    aliasing does in fact occur. To prevent this, you have to use \link DenseBase::eval() eval() \endlink or
    one of the xxxInPlace() functions.
 
diff --git a/doc/TopicAssertions.dox b/doc/TopicAssertions.dox
new file mode 100644
index 000000000..4ead40174
--- /dev/null
+++ b/doc/TopicAssertions.dox
@@ -0,0 +1,108 @@
+namespace Eigen {
+
+/** \page TopicAssertions Assertions
+
+\eigenAutoToc
+
+\section PlainAssert Assertions
+
+The macro eigen_assert is defined to be \c eigen_plain_assert by default. We use eigen_plain_assert instead of \c assert to work around a known bug for GCC <= 4.3. Basically, eigen_plain_assert \a is \c assert.
+
+\subsection RedefineAssert Redefining assertions
+
+Both eigen_assert and eigen_plain_assert are defined in Macros.h. Defining eigen_assert indirectly gives you a chance to change its behavior. You can redefine this macro if you want to do something else such as throwing an exception, and fall back to its default behavior with eigen_plain_assert. The code below tells Eigen to throw an std::runtime_error:
+
+\code
+#include <stdexcept>
+#undef eigen_assert
+#define eigen_assert(x) \
+  if (!x) { throw (std::runtime_error("Put your message here")); }
+\endcode
+
+\subsection DisableAssert Disabling assertions
+
+Assertions cost run time and can be turned off. You can suppress eigen_assert by defining \c EIGEN_NO_DEBUG \b before including Eigen headers. \c EIGEN_NO_DEBUG is undefined by default unless \c NDEBUG is defined.
+
+\section StaticAssert Static assertions
+
+Static assertions are not standardized until C++11. However, in the Eigen library, there are many conditions can and should be detectedat compile time. For instance, we use static assertions to prevent the code below from compiling.
+
+\code
+Matrix3d()  + Matrix4d();   // adding matrices of different sizes
+Matrix4cd() * Vector3cd();  // invalid product known at compile time
+\endcode
+
+Static assertions are defined in StaticAssert.h. If there is native static_assert, we use it. Otherwise, we have implemented an assertion macro that can show a limited range of messages.
+
+One can easily come up with static assertions without messages, such as:
+
+\code
+#define STATIC_ASSERT(x) \
+  switch(0) { case 0: case x:; }
+\endcode
+
+However, the example above obviously cannot tell why the assertion failed. Therefore, we define a \c struct in namespace Eigen::internal to handle available messages.
+
+\code
+template<bool condition>
+struct static_assertion {};
+
+template<>
+struct static_assertion<true>
+{
+  enum {
+    YOU_TRIED_CALLING_A_VECTOR_METHOD_ON_A_MATRIX,
+    YOU_MIXED_VECTORS_OF_DIFFERENT_SIZES,
+    // see StaticAssert.h for all enums.
+  };
+};
+\endcode
+
+And then, we define EIGEN_STATIC_ASSERT(CONDITION,MSG) to access Eigen::internal::static_assertion<bool(CONDITION)>::MSG. If the condition evaluates into \c false, your compiler displays a lot of messages explaining there is no MSG in static_assert<false>. Nevertheless, this is \a not in what we are interested. As you can see, all members of static_assert<true> are ALL_CAPS_AND_THEY_ARE_SHOUTING.
+
+\warning
+When using this macro, MSG should be a member of static_assertion<true>, or the static assertion \b always fails.
+Currently, it can only be used in function scope.
+
+\subsection DerivedStaticAssert Derived static assertions
+
+There are other macros derived from EIGEN_STATIC_ASSERT to enhance readability. Their names are self-explanatory.
+
+- \b EIGEN_STATIC_ASSERT_FIXED_SIZE(TYPE) - passes if \a TYPE is fixed size.
+- \b EIGEN_STATIC_ASSERT_DYNAMIC_SIZE(TYPE) - passes if \a TYPE is dynamic size.
+- \b EIGEN_STATIC_ASSERT_LVALUE(Derived) - failes if \a Derived is read-only.
+- \b EIGEN_STATIC_ASSERT_ARRAYXPR(Derived) - passes if \a Derived is an array expression.
+- <b>EIGEN_STATIC_ASSERT_SAME_XPR_KIND(Derived1, Derived2)</b> - failes if the two expressions are an array one and a matrix one.
+
+Because Eigen handles both fixed-size and dynamic-size expressions, some conditions cannot be clearly determined at compile time. We classify them into strict assertions and permissive assertions.
+
+\subsubsection StrictAssertions Strict assertions
+
+These assertions fail if the condition <b>may not</b> be met. For example, MatrixXd may not be a vector, so it fails EIGEN_STATIC_ASSERT_VECTOR_ONLY.
+
+- \b EIGEN_STATIC_ASSERT_VECTOR_ONLY(TYPE) - passes if \a TYPE must be a vector type.
+- <b>EIGEN_STATIC_ASSERT_VECTOR_SPECIFIC_SIZE(TYPE, SIZE)</b> - passes if \a TYPE must be a vector of the given size.
+- <b>EIGEN_STATIC_ASSERT_MATRIX_SPECIFIC_SIZE(TYPE, ROWS, COLS)</b> - passes if \a TYPE must be a matrix with given rows and columns.
+
+\subsubsection PermissiveAssertions Permissive assertions
+
+These assertions fail if the condition \b cannot be met. For example, MatrixXd and Matrix4d may have the same size, so they pass EIGEN_STATIC_ASSERT_SAME_MATRIX_SIZE.
+
+- \b EIGEN_STATIC_ASSERT_SAME_VECTOR_SIZE(TYPE0,TYPE1) - fails if the two vector expression types must have different sizes.
+- \b EIGEN_STATIC_ASSERT_SAME_MATRIX_SIZE(TYPE0,TYPE1) - fails if the two matrix expression types must have different sizes.
+- \b EIGEN_STATIC_ASSERT_SIZE_1x1(TYPE) - fails if \a TYPE cannot be an 1x1 expression.
+
+See StaticAssert.h for details such as what messages they throw.
+
+\subsection DisableStaticAssert Disabling static assertions
+
+If \c EIGEN_NO_STATIC_ASSERT is defined, static assertions turn into <tt>eigen_assert</tt>'s, working like:
+
+\code
+#define EIGEN_STATIC_ASSERT(CONDITION,MSG) eigen_assert((CONDITION) && #MSG);
+\endcode
+
+This saves compile time but consumes more run time. \c EIGEN_NO_STATIC_ASSERT is undefined by default.
+
+*/
+}
diff --git a/doc/I06_TopicEigenExpressionTemplates.dox b/doc/TopicEigenExpressionTemplates.dox
index b31fd47f9..b31fd47f9 100644
--- a/doc/I06_TopicEigenExpressionTemplates.dox
+++ b/doc/TopicEigenExpressionTemplates.dox
diff --git a/doc/I01_TopicLazyEvaluation.dox b/doc/TopicLazyEvaluation.dox
index 393bc41d8..393bc41d8 100644
--- a/doc/I01_TopicLazyEvaluation.dox
+++ b/doc/TopicLazyEvaluation.dox
diff --git a/doc/TopicLinearAlgebraDecompositions.dox b/doc/TopicLinearAlgebraDecompositions.dox
index faa564b93..8649cc27b 100644
--- a/doc/TopicLinearAlgebraDecompositions.dox
+++ b/doc/TopicLinearAlgebraDecompositions.dox
@@ -1,12 +1,13 @@
 namespace Eigen {
 
-/** \page TopicLinearAlgebraDecompositions Linear algebra and decompositions
+/** \eigenManualPage TopicLinearAlgebraDecompositions Catalogue of dense decompositions
 
+This page presents a catalogue of the dense matrix decompositions offered by Eigen.
+For an introduction on linear solvers and decompositions, check this \link TutorialLinearAlgebra page \endlink.
 
 \section TopicLinAlgBigTable Catalogue of decompositions offered by Eigen
 
 <table class="manual-vl">
-
     <tr>
         <th class="meta"></th>
         <th class="meta" colspan="5">Generic information, not Eigen-specific</th>
diff --git a/doc/I08_Resizing.dox b/doc/TopicResizing.dox
index c323e17ad..c323e17ad 100644
--- a/doc/I08_Resizing.dox
+++ b/doc/TopicResizing.dox
diff --git a/doc/I07_TopicScalarTypes.dox b/doc/TopicScalarTypes.dox
index 2ff03c198..2ff03c198 100644
--- a/doc/I07_TopicScalarTypes.dox
+++ b/doc/TopicScalarTypes.dox
diff --git a/doc/I09_Vectorization.dox b/doc/TopicVectorization.dox
index 274d0451b..274d0451b 100644
--- a/doc/I09_Vectorization.dox
+++ b/doc/TopicVectorization.dox
diff --git a/doc/C05_TutorialAdvancedInitialization.dox b/doc/TutorialAdvancedInitialization.dox
index 4f27f1e4d..50374d0d0 100644
--- a/doc/C05_TutorialAdvancedInitialization.dox
+++ b/doc/TutorialAdvancedInitialization.dox
@@ -1,20 +1,12 @@
 namespace Eigen {
 
-/** \page TutorialAdvancedInitialization Tutorial page 5 - Advanced initialization
-    \ingroup Tutorial
-
-\li \b Previous: \ref TutorialBlockOperations
-\li \b Next: \ref TutorialLinearAlgebra
+/** \eigenManualPage TutorialAdvancedInitialization Advanced initialization
 
 This page discusses several advanced methods for initializing matrices. It gives more details on the
 comma-initializer, which was introduced before. It also explains how to get special matrices such as the
 identity matrix and the zero matrix.
 
-\b Table \b of \b contents
-  - \ref TutorialAdvancedInitializationCommaInitializer
-  - \ref TutorialAdvancedInitializationSpecialMatrices
-  - \ref TutorialAdvancedInitializationTemporaryObjects
-
+\eigenAutoToc
 
 \section TutorialAdvancedInitializationCommaInitializer The comma initializer
 
@@ -165,8 +157,6 @@ The \link CommaInitializer::finished() finished() \endlink method is necessary h
 object once the comma initialization of our temporary submatrix is done.
 
 
-\li \b Next: \ref TutorialLinearAlgebra
-
 */
 
 }
diff --git a/doc/C03_TutorialArrayClass.dox b/doc/TutorialArrayClass.dox
index a1d8d6985..6432684aa 100644
--- a/doc/C03_TutorialArrayClass.dox
+++ b/doc/TutorialArrayClass.dox
@@ -1,23 +1,12 @@
 namespace Eigen {
 
-/** \page TutorialArrayClass Tutorial page 3 - The %Array class and coefficient-wise operations
-    \ingroup Tutorial
+/** \eigenManualPage TutorialArrayClass The Array class and coefficient-wise operations
 
-\li \b Previous: \ref TutorialMatrixArithmetic
-\li \b Next: \ref TutorialBlockOperations
-
-This tutorial aims to provide an overview and explanations on how to use
+This page aims to provide an overview and explanations on how to use
 Eigen's Array class.
 
-\b Table \b of \b contents
-  - \ref TutorialArrayClassIntro
-  - \ref TutorialArrayClassTypes
-  - \ref TutorialArrayClassAccess
-  - \ref TutorialArrayClassAddSub
-  - \ref TutorialArrayClassMult
-  - \ref TutorialArrayClassCwiseOther
-  - \ref TutorialArrayClassConvert
-
+\eigenAutoToc
+  
 \section TutorialArrayClassIntro What is the Array class?
 
 The Array class provides general-purpose arrays, as opposed to the Matrix class which
@@ -122,7 +111,7 @@ arrays can be multiplied if and only if they have the same dimensions.
 The Array class defines other coefficient-wise operations besides the addition, subtraction and multiplication
 operators described above. For example, the \link ArrayBase::abs() .abs() \endlink method takes the absolute
 value of each coefficient, while \link ArrayBase::sqrt() .sqrt() \endlink computes the square root of the
-coefficients. If you have two arrays of the same size, you can call \link ArrayBase::min() .min() \endlink to
+coefficients. If you have two arrays of the same size, you can call \link ArrayBase::min(const Eigen::ArrayBase<OtherDerived>&) const .min(.) \endlink to
 construct the array whose coefficients are the minimum of the corresponding coefficients of the two given
 arrays. These operations are illustrated in the following example.
 
@@ -168,8 +157,8 @@ The following example shows how to use array operations on a Matrix object by em
 * to multiply them coefficient-wise and assigns the result to the matrix variable \c result (this is legal
 because Eigen allows assigning array expressions to matrix variables). 
 
-As a matter of fact, this usage case is so common that Eigen provides a \link MatrixBase::cwiseProduct()
-.cwiseProduct() \endlink method for matrices to compute the coefficient-wise product. This is also shown in
+As a matter of fact, this usage case is so common that Eigen provides a \link MatrixBase::cwiseProduct() const
+.cwiseProduct(.) \endlink method for matrices to compute the coefficient-wise product. This is also shown in
 the example program.
 
 <table class="example">
@@ -198,8 +187,6 @@ expression <tt>(m.array() * n.array()).matrix() * m</tt> computes the coefficien
 \verbinclude Tutorial_ArrayClass_interop.out
 </td></tr></table>
 
-\li \b Next: \ref TutorialBlockOperations
-
 */
 
 }
diff --git a/doc/C04_TutorialBlockOperations.dox b/doc/TutorialBlockOperations.dox
index eac0eaa59..a2d8c97cc 100644
--- a/doc/C04_TutorialBlockOperations.dox
+++ b/doc/TutorialBlockOperations.dox
@@ -1,22 +1,13 @@
 namespace Eigen {
 
-/** \page TutorialBlockOperations Tutorial page 4 - %Block operations
-    \ingroup Tutorial
+/** \eigenManualPage TutorialBlockOperations Block operations
 
-\li \b Previous: \ref TutorialArrayClass
-\li \b Next: \ref TutorialAdvancedInitialization
-
-This tutorial page explains the essentials of block operations.
+This page explains the essentials of block operations.
 A block is a rectangular part of a matrix or array. Blocks expressions can be used both
 as rvalues and as lvalues. As usual with Eigen expressions, this abstraction has zero runtime cost
 provided that you let your compiler optimize.
 
-\b Table \b of \b contents
-  - \ref TutorialBlockOperationsUsing
-  - \ref TutorialBlockOperationsSyntaxColumnRows
-  - \ref TutorialBlockOperationsSyntaxCorners
-  - \ref TutorialBlockOperationsSyntaxVectors
-
+\eigenAutoToc
 
 \section TutorialBlockOperationsUsing Using block operations
 
@@ -232,8 +223,6 @@ An example is presented below:
 \verbinclude Tutorial_BlockOperations_vector.out
 </td></tr></table>
 
-\li \b Next: \ref TutorialAdvancedInitialization
-
 */
 
 }
diff --git a/doc/C08_TutorialGeometry.dox b/doc/TutorialGeometry.dox
index b9e9eba12..372a275de 100644
--- a/doc/C08_TutorialGeometry.dox
+++ b/doc/TutorialGeometry.dox
@@ -1,18 +1,10 @@
 namespace Eigen {
 
-/** \page TutorialGeometry Tutorial page 8 - Geometry
-    \ingroup Tutorial
+/** \eigenManualPage TutorialGeometry Space transformations
 
-\li \b Previous: \ref TutorialReductionsVisitorsBroadcasting
-\li \b Next: \ref TutorialSparse
+In this page, we will introduce the many possibilities offered by the \ref Geometry_Module "geometry module" to deal with 2D and 3D rotations and projective or affine transformations.
 
-In this tutorial, we will briefly introduce the many possibilities offered by the \ref Geometry_Module "geometry module", namely 2D and 3D rotations and projective or affine transformations.
-
-\b Table \b of \b contents
-  - \ref TutorialGeoElementaryTransformations
-  - \ref TutorialGeoCommontransformationAPI
-  - \ref TutorialGeoTransform
-  - \ref TutorialGeoEulerAngles
+\eigenAutoToc
 
 Eigen's Geometry module provides two different kinds of geometric transformations:
   - Abstract transformations, such as rotations (represented by \ref AngleAxis "angle and axis" or by a \ref Quaternion "quaternion"), \ref Translation "translations", \ref Scaling "scalings". These transformations are NOT represented as matrices, but you can nevertheless mix them with matrices and vectors in expressions, and convert them to matrices if you wish.
@@ -135,7 +127,7 @@ VectorNf vec1, vec2;
 vec2 = t.linear() * vec1;\endcode</td></tr>
 <tr><td>
 Apply a \em general transformation \n to a \b normal \b vector
-(<a href="http://www.cgafaq.info/wiki/Transforming_normals">explanations</a>)</td><td>\code
+(<a href="http://femto.cs.uiuc.edu/faqs/cga-faq.html#S5.27">explanations</a>)</td><td>\code
 VectorNf n1, n2;
 MatrixNf normalMatrix = t.linear().inverse().transpose();
 n2 = (normalMatrix * n1).normalized();\endcode</td></tr>
@@ -178,7 +170,7 @@ matNxN = t.linear();
 \endcode</td></tr>
 <tr><td>
 extract the rotation matrix</td><td>\code
-matNxN = t.extractRotation();
+matNxN = t.rotation();
 \endcode</td></tr>
 </table>
 
@@ -244,8 +236,6 @@ m = AngleAxisf(angle1, Vector3f::UnitZ())
 \endcode</td></tr>
 </table>
 
-\li \b Next: \ref TutorialSparse
-
 */
 
 }
diff --git a/doc/C06_TutorialLinearAlgebra.dox b/doc/TutorialLinearAlgebra.dox
index e8b3b7953..b09f3543e 100644
--- a/doc/C06_TutorialLinearAlgebra.dox
+++ b/doc/TutorialLinearAlgebra.dox
@@ -1,24 +1,12 @@
 namespace Eigen {
 
-/** \page TutorialLinearAlgebra Tutorial page 6 - Linear algebra and decompositions
-    \ingroup Tutorial
+/** \eigenManualPage TutorialLinearAlgebra Linear algebra and decompositions
 
-\li \b Previous: \ref TutorialAdvancedInitialization
-\li \b Next: \ref TutorialReductionsVisitorsBroadcasting
-
-This tutorial explains how to solve linear systems, compute various decompositions such as LU,
-QR, %SVD, eigendecompositions... for more advanced topics, don't miss our special page on
-\ref TopicLinearAlgebraDecompositions "this topic".
-
-\b Table \b of \b contents
-  - \ref TutorialLinAlgBasicSolve
-  - \ref TutorialLinAlgSolutionExists
-  - \ref TutorialLinAlgEigensolving
-  - \ref TutorialLinAlgInverse
-  - \ref TutorialLinAlgLeastsquares
-  - \ref TutorialLinAlgSeparateComputation
-  - \ref TutorialLinAlgRankRevealing
+This page explains how to solve linear systems, compute various decompositions such as LU,
+QR, %SVD, eigendecompositions... After reading this page, don't miss our
+\link TopicLinearAlgebraDecompositions catalogue \endlink of dense matrix decompositions.
 
+\eigenAutoToc
 
 \section TutorialLinAlgBasicSolve Basic linear solving
 
@@ -262,8 +250,6 @@ decomposition after you've changed the threshold.
 </tr>
 </table>
 
-\li \b Next: \ref TutorialReductionsVisitorsBroadcasting
-
 */
 
 }
diff --git a/doc/C10_TutorialMapClass.dox b/doc/TutorialMapClass.dox
index 09e792792..f8fb0fd2f 100644
--- a/doc/C10_TutorialMapClass.dox
+++ b/doc/TutorialMapClass.dox
@@ -1,27 +1,19 @@
 namespace Eigen {
 
-/** \page TutorialMapClass Tutorial page 10 - Interfacing with C/C++ arrays and external libraries: the %Map class
+/** \eigenManualPage TutorialMapClass Interfacing with raw buffers: the Map class
 
-\ingroup Tutorial
+This page explains how to work with "raw" C/C++ arrays.
+This can be useful in a variety of contexts, particularly when "importing" vectors and matrices from other libraries into %Eigen.
 
-\li \b Previous: \ref TutorialSparse
-\li \b Next: \ref TODO
-
-This tutorial page explains how to work with "raw" C++ arrays.  This can be useful in a variety of contexts, particularly when "importing" vectors and matrices from other libraries into Eigen.
-
-\b Table \b of \b contents
-  - \ref TutorialMapIntroduction
-  - \ref TutorialMapTypes
-  - \ref TutorialMapUsing
-  - \ref TutorialMapPlacementNew
+\eigenAutoToc
 
 \section TutorialMapIntroduction Introduction
 
-Occasionally you may have a pre-defined array of numbers that you want to use within Eigen as a vector or matrix. While one option is to make a copy of the data, most commonly you probably want to re-use this memory as an Eigen type. Fortunately, this is very easy with the Map class.
+Occasionally you may have a pre-defined array of numbers that you want to use within %Eigen as a vector or matrix. While one option is to make a copy of the data, most commonly you probably want to re-use this memory as an %Eigen type. Fortunately, this is very easy with the Map class.
 
 \section TutorialMapTypes Map types and declaring Map variables
 
-A Map object has a type defined by its Eigen equivalent:
+A Map object has a type defined by its %Eigen equivalent:
 \code
 Map<Matrix<typename Scalar, int RowsAtCompileTime, int ColsAtCompileTime> >
 \endcode
@@ -57,7 +49,7 @@ However, Stride is even more flexible than this; for details, see the documentat
 
 \section TutorialMapUsing Using Map variables
 
-You can use a Map object just like any other Eigen type:
+You can use a Map object just like any other %Eigen type:
 <table class="example">
 <tr><th>Example:</th><th>Output:</th></tr>
 <tr>
@@ -65,7 +57,7 @@ You can use a Map object just like any other Eigen type:
 <td>\verbinclude Tutorial_Map_using.out </td>
 </table>
 
-However, when writing functions taking Eigen types, it is important to realize that a Map type is \em not identical to its Dense equivalent.  See \ref TopicFunctionTakingEigenTypesMultiarguments for details.
+All %Eigen functions are written to accept Map objects just like other %Eigen types. However, when writing your own functions taking %Eigen types, this does \em not happen automatically: a Map type is not identical to its Dense equivalent.  See \ref TopicFunctionTakingEigenTypes for details.
 
 \section TutorialMapPlacementNew Changing the mapped array
 
@@ -89,8 +81,6 @@ for (int i = 0; i < n_matrices; i++)
 }
 \endcode
 
-\li \b Next: \ref TODO
-
 */
 
 }
diff --git a/doc/C02_TutorialMatrixArithmetic.dox b/doc/TutorialMatrixArithmetic.dox
index b04821a87..5fc569a30 100644
--- a/doc/C02_TutorialMatrixArithmetic.dox
+++ b/doc/TutorialMatrixArithmetic.dox
@@ -1,24 +1,11 @@
 namespace Eigen {
 
-/** \page TutorialMatrixArithmetic Tutorial page 2 - %Matrix and vector arithmetic
-    \ingroup Tutorial
+/** \eigenManualPage TutorialMatrixArithmetic Matrix and vector arithmetic
 
-\li \b Previous: \ref TutorialMatrixClass
-\li \b Next: \ref TutorialArrayClass
-
-This tutorial aims to provide an overview and some details on how to perform arithmetic
+This page aims to provide an overview and some details on how to perform arithmetic
 between matrices, vectors and scalars with Eigen.
 
-\b Table \b of \b contents
-  - \ref TutorialArithmeticIntroduction
-  - \ref TutorialArithmeticAddSub
-  - \ref TutorialArithmeticScalarMulDiv
-  - \ref TutorialArithmeticMentionXprTemplates
-  - \ref TutorialArithmeticTranspose
-  - \ref TutorialArithmeticMatrixMul
-  - \ref TutorialArithmeticDotAndCross
-  - \ref TutorialArithmeticRedux
-  - \ref TutorialArithmeticValidity
+\eigenAutoToc
 
 \section TutorialArithmeticIntroduction Introduction
 
@@ -222,8 +209,6 @@ Eigen then uses runtime assertions. This means that the program will abort with
 
 For more details on this topic, see \ref TopicAssertions "this page".
 
-\li \b Next: \ref TutorialArrayClass
-
 */
 
 }
diff --git a/doc/C01_TutorialMatrixClass.dox b/doc/TutorialMatrixClass.dox
index 4860616e5..7ea0cd789 100644
--- a/doc/C01_TutorialMatrixClass.dox
+++ b/doc/TutorialMatrixClass.dox
@@ -1,27 +1,8 @@
 namespace Eigen {
 
-/** \page TutorialMatrixClass Tutorial page 1 - The %Matrix class
+/** \eigenManualPage TutorialMatrixClass The Matrix class
 
-\ingroup Tutorial
-
-\li \b Previous: \ref GettingStarted
-\li \b Next: \ref TutorialMatrixArithmetic
-
-We assume that you have already read the quick \link GettingStarted "getting started" \endlink tutorial.
-This page is the first one in a much longer multi-page tutorial.
-
-\b Table \b of \b contents
-  - \ref TutorialMatrixFirst3Params
-  - \ref TutorialMatrixVectors
-  - \ref TutorialMatrixDynamic
-  - \ref TutorialMatrixConstructors
-  - \ref TutorialMatrixCoeffAccessors
-  - \ref TutorialMatrixCommaInitializer
-  - \ref TutorialMatrixSizesResizing
-  - \ref TutorialMatrixAssignment
-  - \ref TutorialMatrixFixedVsDynamic
-  - \ref TutorialMatrixOptTemplParams
-  - \ref TutorialMatrixTypedefs
+\eigenAutoToc
 
 In Eigen, all matrices and vectors are objects of the Matrix template class.
 Vectors are just a special case of matrices, with either 1 row or 1 column.
@@ -98,8 +79,8 @@ Matrix3f a;
 MatrixXf b;
 \endcode
 Here,
-\li \c a is a 3x3 matrix, with a static float[9] array of uninitialized coefficients,
-\li \c b is a dynamic-size matrix whose size is currently 0x0, and whose array of
+\li \c a is a 3-by-3 matrix, with a plain float[9] array of uninitialized coefficients,
+\li \c b is a dynamic-size matrix whose size is currently 0-by-0, and whose array of
 coefficients hasn't yet been allocated at all.
 
 Constructors taking sizes are also available. For matrices, the number of rows is always passed first.
@@ -216,7 +197,7 @@ The simple answer is: use fixed
 sizes for very small sizes where you can, and use dynamic sizes for larger sizes or where you have to. For small sizes,
 especially for sizes smaller than (roughly) 16, using fixed sizes is hugely beneficial
 to performance, as it allows Eigen to avoid dynamic memory allocation and to unroll
-loops. Internally, a fixed-size Eigen matrix is just a plain static array, i.e. doing
+loops. Internally, a fixed-size Eigen matrix is just a plain array, i.e. doing
 \code Matrix4f mymatrix; \endcode
 really amounts to just doing
 \code float mymatrix[16]; \endcode
@@ -231,8 +212,9 @@ member variables.
 The limitation of using fixed sizes, of course, is that this is only possible
 when you know the sizes at compile time. Also, for large enough sizes, say for sizes
 greater than (roughly) 32, the performance benefit of using fixed sizes becomes negligible.
-Worse, trying to create a very large matrix using fixed sizes could result in a stack overflow,
-since Eigen will try to allocate the array as a static array, which by default goes on the stack.
+Worse, trying to create a very large matrix using fixed sizes inside a function could result in a
+stack overflow, since Eigen will try to allocate the array automatically as a local variable, and
+this is normally done on the stack.
 Finally, depending on circumstances, Eigen can also be more aggressive trying to vectorize
 (use SIMD instructions) when dynamic sizes are used, see \ref TopicVectorization "Vectorization".
 
@@ -258,7 +240,7 @@ Matrix<typename Scalar,
 \li \c MaxRowsAtCompileTime and \c MaxColsAtCompileTime are useful when you want to specify that, even though
       the exact sizes of your matrices are not known at compile time, a fixed upper bound is known at
       compile time. The biggest reason why you might want to do that is to avoid dynamic memory allocation.
-      For example the following matrix type uses a static array of 12 floats, without dynamic memory allocation:
+      For example the following matrix type uses a plain array of 12 floats, without dynamic memory allocation:
       \code
       Matrix<float, Dynamic, Dynamic, 0, 3, 4>
       \endcode
@@ -277,7 +259,6 @@ Where:
     defined for these five types doesn't mean that they are the only supported scalar types. For example,
     all standard integer types are supported, see \ref TopicScalarTypes "Scalar types".
 
-\li \b Next: \ref TutorialMatrixArithmetic
 
 */
 
diff --git a/doc/C07_TutorialReductionsVisitorsBroadcasting.dox b/doc/TutorialReductionsVisitorsBroadcasting.dox
index f3879b8b9..992cf6f34 100644
--- a/doc/C07_TutorialReductionsVisitorsBroadcasting.dox
+++ b/doc/TutorialReductionsVisitorsBroadcasting.dox
@@ -1,25 +1,11 @@
 namespace Eigen {
 
-/** \page TutorialReductionsVisitorsBroadcasting Tutorial page 7 - Reductions, visitors and broadcasting
-    \ingroup Tutorial
+/** \eigenManualPage TutorialReductionsVisitorsBroadcasting Reductions, visitors and broadcasting
 
-\li \b Previous: \ref TutorialLinearAlgebra
-\li \b Next: \ref TutorialGeometry
-
-This tutorial explains Eigen's reductions, visitors and broadcasting and how they are used with
+This page explains Eigen's reductions, visitors and broadcasting and how they are used with
 \link MatrixBase matrices \endlink and \link ArrayBase arrays \endlink.
 
-\b Table \b of \b contents
-  - \ref TutorialReductionsVisitorsBroadcastingReductions
-    - \ref TutorialReductionsVisitorsBroadcastingReductionsNorm
-    - \ref TutorialReductionsVisitorsBroadcastingReductionsBool
-    - \ref TutorialReductionsVisitorsBroadcastingReductionsUserdefined
-  - \ref TutorialReductionsVisitorsBroadcastingVisitors
-  - \ref TutorialReductionsVisitorsBroadcastingPartialReductions
-    - \ref TutorialReductionsVisitorsBroadcastingPartialReductionsCombined
-  - \ref TutorialReductionsVisitorsBroadcastingBroadcasting
-    - \ref TutorialReductionsVisitorsBroadcastingBroadcastingCombined
-
+\eigenAutoToc
 
 \section TutorialReductionsVisitorsBroadcastingReductions Reductions
 In Eigen, a reduction is a function taking a matrix or array, and returning a single
@@ -266,8 +252,6 @@ this operation is a row-vector where each coefficient is the squared Euclidean d
   - Finally, <tt>minCoeff(&index)</tt> is used to obtain the index of the column in <tt>m</tt> that is closest to <tt>v</tt> in terms of Euclidean
 distance.
 
-\li \b Next: \ref TutorialGeometry
-
 */
 
 }
diff --git a/doc/C09_TutorialSparse.dox b/doc/TutorialSparse.dox
index 34154bd0d..fa2a3ad8b 100644
--- a/doc/C09_TutorialSparse.dox
+++ b/doc/TutorialSparse.dox
@@ -1,37 +1,23 @@
 namespace Eigen {
 
-/** \page TutorialSparse Tutorial page 9 - Sparse Matrix
-    \ingroup Tutorial
+/** \eigenManualPage TutorialSparse Sparse matrix manipulations
 
-\li \b Previous: \ref TutorialGeometry
-\li \b Next: \ref TutorialMapClass
-
-\b Table \b of \b contents \n
-  - \ref TutorialSparseIntro
-  - \ref TutorialSparseExample "Example"
-  - \ref TutorialSparseSparseMatrix
-  - \ref TutorialSparseFilling
-  - \ref TutorialSparseDirectSolvers
-  - \ref TutorialSparseFeatureSet
-    - \ref TutorialSparse_BasicOps
-    - \ref TutorialSparse_Products
-    - \ref TutorialSparse_TriangularSelfadjoint
-    - \ref TutorialSparse_Submat
-
-
-<hr>
+\eigenAutoToc
 
 Manipulating and solving sparse problems involves various modules which are summarized below:
 
 <table class="manual">
 <tr><th>Module</th><th>Header file</th><th>Contents</th></tr>
-<tr><td>\link Sparse_Module SparseCore \endlink</td><td>\code#include <Eigen/SparseCore>\endcode</td><td>SparseMatrix and SparseVector classes, matrix assembly, basic sparse linear algebra (including sparse triangular solvers)</td></tr>
+<tr><td>\link SparseCore_Module SparseCore \endlink</td><td>\code#include <Eigen/SparseCore>\endcode</td><td>SparseMatrix and SparseVector classes, matrix assembly, basic sparse linear algebra (including sparse triangular solvers)</td></tr>
 <tr><td>\link SparseCholesky_Module SparseCholesky \endlink</td><td>\code#include <Eigen/SparseCholesky>\endcode</td><td>Direct sparse LLT and LDLT Cholesky factorization to solve sparse self-adjoint positive definite problems</td></tr>
+<tr><td>\link SparseLU_Module SparseLU \endlink</td><td>\code #include<Eigen/SparseLU> \endcode</td>
+<td>%Sparse LU factorization to solve general square sparse systems</td></tr>
+<tr><td>\link SparseQR_Module SparseQR \endlink</td><td>\code #include<Eigen/SparseQR>\endcode </td><td>%Sparse QR factorization for solving sparse linear least-squares problems</td></tr>
 <tr><td>\link IterativeLinearSolvers_Module IterativeLinearSolvers \endlink</td><td>\code#include <Eigen/IterativeLinearSolvers>\endcode</td><td>Iterative solvers to solve large general linear square problems (including self-adjoint positive definite problems)</td></tr>
-<tr><td></td><td>\code#include <Eigen/Sparse>\endcode</td><td>Includes all the above modules</td></tr>
+<tr><td>\link Sparse_Module Sparse \endlink</td><td>\code#include <Eigen/Sparse>\endcode</td><td>Includes all the above modules</td></tr>
 </table>
 
-\section TutorialSparseIntro Sparse matrix representation
+\section TutorialSparseIntro Sparse matrix format
 
 In many applications (e.g., finite element methods) it is common to deal with very large matrices where only a few coefficients are different from zero.  In such cases, memory consumption can be reduced and performance increased by using a specialized representation storing only the nonzero coefficients. Such a matrix is called a sparse matrix.
 
@@ -97,7 +83,7 @@ There is no notion of compressed/uncompressed mode for a SparseVector.
 
 \section TutorialSparseExample First example
 
-Before describing each individual class, let's start with the following typical example: solving the Lapace equation \f$ \nabla u = 0 \f$ on a regular 2D grid using a finite difference scheme and Dirichlet boundary conditions.
+Before describing each individual class, let's start with the following typical example: solving the Laplace equation \f$ \nabla u = 0 \f$ on a regular 2D grid using a finite difference scheme and Dirichlet boundary conditions.
 Such problem can be mathematically expressed as a linear problem of the form \f$ Ax=b \f$ where \f$ x \f$ is the vector of \c m unknowns (in our case, the values of the pixels), \f$ b \f$ is the right hand side vector resulting from the boundary conditions, and \f$ A \f$ is an \f$ m \times m \f$ matrix containing only a few non-zero elements resulting from the discretization of the Laplacian operator.
 
 <table class="manual">
@@ -130,7 +116,7 @@ Describing the \a buildProblem and \a save functions is out of the scope of this
 
 The SparseMatrix and SparseVector classes take three template arguments:
  * the scalar type (e.g., double)
- * the storage order (ColMajor or RowMajor, the default is RowMajor)
+ * the storage order (ColMajor or RowMajor, the default is ColMajor)
  * the inner index type (default is \c int).
 
 As for dense Matrix objects, constructors takes the size of the object.
@@ -211,7 +197,7 @@ Here is a typical usage example:
 \code
 typedef Eigen::Triplet<double> T;
 std::vector<T> tripletList;
-triplets.reserve(estimation_of_entries);
+tripletList.reserve(estimation_of_entries);
 for(...)
 {
   // ...
@@ -241,102 +227,10 @@ A typical scenario of this approach is illustrated bellow:
 - The line 5 suppresses the remaining empty space and transforms the matrix into a compressed column storage.
 
 
-\section TutorialSparseDirectSolvers Solving linear problems
-
-%Eigen currently provides a limited set of built-in solvers, as well as wrappers to external solver libraries.
-They are summarized in the following table:
-
-<table class="manual">
-<tr><th>Class</th><th>Module</th><th>Solver kind</th><th>Matrix kind</th><th>Features related to performance</th>
-    <th>Dependencies,License</th><th class="width20em"><p>Notes</p></th></tr>
-<tr><td>SimplicialLLT    </td><td>\link SparseCholesky_Module SparseCholesky \endlink</td><td>Direct LLt factorization</td><td>SPD</td><td>Fill-in reducing</td>
-    <td>built-in, LGPL</td>
-    <td>SimplicialLDLT is often preferable</td></tr>
-<tr><td>SimplicialLDLT   </td><td>\link SparseCholesky_Module SparseCholesky \endlink</td><td>Direct LDLt factorization</td><td>SPD</td><td>Fill-in reducing</td>
-    <td>built-in, LGPL</td>
-    <td>Recommended for very sparse and not too large problems (e.g., 2D Poisson eq.)</td></tr>
-<tr><td>ConjugateGradient</td><td>\link IterativeLinearSolvers_Module IterativeLinearSolvers \endlink</td><td>Classic iterative CG</td><td>SPD</td><td>Preconditionning</td>
-    <td>built-in, LGPL</td>
-    <td>Recommended for large symmetric problems (e.g., 3D Poisson eq.)</td></tr>
-<tr><td>BiCGSTAB</td><td>\link IterativeLinearSolvers_Module IterativeLinearSolvers \endlink</td><td>Iterative stabilized bi-conjugate gradient</td><td>Square</td><td>Preconditionning</td>
-    <td>built-in, LGPL</td>
-    <td>Might not always converge</td></tr>
-
-
-<tr><td>PastixLLT \n PastixLDLT \n PastixLU</td><td>\link PaStiXSupport_Module PaStiXSupport \endlink</td><td>Direct LLt, LDLt, LU factorizations</td><td>SPD \n SPD \n Square</td><td>Fill-in reducing, Leverage fast dense algebra, Multithreading</td>
-    <td>Requires the <a href="http://pastix.gforge.inria.fr">PaStiX</a> package, \b CeCILL-C </td>
-    <td>optimized for tough problems and symmetric patterns</td></tr>
-<tr><td>CholmodSupernodalLLT</td><td>\link CholmodSupport_Module CholmodSupport \endlink</td><td>Direct LLt factorization</td><td>SPD</td><td>Fill-in reducing, Leverage fast dense algebra</td>
-    <td>Requires the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">SuiteSparse</a> package, \b GPL </td>
-    <td></td></tr>
-<tr><td>UmfPackLU</td><td>\link UmfPackSupport_Module UmfPackSupport \endlink</td><td>Direct LU factorization</td><td>Square</td><td>Fill-in reducing, Leverage fast dense algebra</td>
-    <td>Requires the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">SuiteSparse</a> package, \b GPL </td>
-    <td></td></tr>
-<tr><td>SuperLU</td><td>\link SuperLUSupport_Module SuperLUSupport \endlink</td><td>Direct LU factorization</td><td>Square</td><td>Fill-in reducing, Leverage fast dense algebra</td>
-    <td>Requires the <a href="http://crd-legacy.lbl.gov/~xiaoye/SuperLU/">SuperLU</a> library, (BSD-like)</td>
-    <td></td></tr>
-</table>
-
-Here \c SPD means symmetric positive definite.
-
-All these solvers follow the same general concept.
-Here is a typical and general example:
-\code
-#include <Eigen/RequiredModuleName>
-// ...
-SparseMatrix<double> A;
-// fill A
-VectorXd b, x;
-// fill b
-// solve Ax = b
-SolverClassName<SparseMatrix<double> > solver;
-solver.compute(A);
-if(solver.info()!=Succeeded) {
-  // decomposition failed
-  return;
-}
-x = solver.solve(b);
-if(solver.info()!=Succeeded) {
-  // solving failed
-  return;
-}
-// solve for another right hand side:
-x1 = solver.solve(b1);
-\endcode
-
-For \c SPD solvers, a second optional template argument allows to specify which triangular part have to be used, e.g.:
-
-\code
-#include <Eigen/IterativeLinearSolvers>
-
-ConjugateGradient<SparseMatrix<double>, Eigen::Upper> solver;
-x = solver.compute(A).solve(b);
-\endcode
-In the above example, only the upper triangular part of the input matrix A is considered for solving. The opposite triangle might either be empty or contain arbitrary values.
-
-In the case where multiple problems with the same sparcity pattern have to be solved, then the "compute" step can be decomposed as follow:
-\code
-SolverClassName<SparseMatrix<double> > solver;
-solver.analyzePattern(A);   // for this step the numerical values of A are not used
-solver.factorize(A);
-x1 = solver.solve(b1);
-x2 = solver.solve(b2);
-...
-A = ...;                    // modify the values of the nonzeros of A, the nonzeros pattern must stay unchanged
-solver.factorize(A);
-x1 = solver.solve(b1);
-x2 = solver.solve(b2);
-...
-\endcode
-The compute() method is equivalent to calling both analyzePattern() and factorize().
-
-Finally, each solver provides some specific features, such as determinant, access to the factors, controls of the iterations, and so on.
-More details are availble in the documentations of the respective classes.
-
 
 \section TutorialSparseFeatureSet Supported operators and functions
 
-Because of their special storage format, sparse matrices cannot offer the same level of flexbility than dense matrices.
+Because of their special storage format, sparse matrices cannot offer the same level of flexibility than dense matrices.
 In Eigen's sparse module we chose to expose only the subset of the dense matrix API which can be efficiently implemented.
 In the following \em sm denotes a sparse matrix, \em sv a sparse vector, \em dm a dense matrix, and \em dv a dense vector.
 
@@ -359,12 +253,15 @@ SparseMatrix<double> A, B;
 B = SparseMatrix<double>(A.transpose()) + A;
 \endcode
 
-Binary coefficient wise operators can also mix sparse and dense expressions:
+Some binary coefficient-wise operators can also mix sparse and dense expressions:
 \code
 sm2 = sm1.cwiseProduct(dm1);
-dm2 = sm1 + dm1;
+dm1 += sm1;
 \endcode
 
+However, it is not yet possible to add a sparse and a dense matrix as in <tt>dm2 = sm1 + dm1</tt>.
+Please write this as the equivalent <tt>dm2 = dm1; dm2 += sm1</tt> (we plan to lift this restriction
+in the next release of %Eigen).
 
 %Sparse expressions also support transposition:
 \code
@@ -396,9 +293,9 @@ sm3 = 4 * sm1.adjoint() * sm2;
     \endcode
     The second algorithm prunes on the fly the explicit zeros, or the values smaller than a given threshold. It is enabled and controlled through the prune() functions:
     \code
-sm3 = (sm1 * sm2).prune();                  // removes numerical zeros
-sm3 = (sm1 * sm2).prune(ref);               // removes elements much smaller than ref
-sm3 = (sm1 * sm2).prune(ref,epsilon);       // removes elements smaller than ref*epsilon
+sm3 = (sm1 * sm2).pruned();                  // removes numerical zeros
+sm3 = (sm1 * sm2).pruned(ref);               // removes elements much smaller than ref
+sm3 = (sm1 * sm2).pruned(ref,epsilon);       // removes elements smaller than ref*epsilon
     \endcode
 
   - \b permutations. Finally, permutations can be applied to sparse matrices too:
@@ -437,18 +334,7 @@ sm2 = A.selfadjointView<Upper>().twistedBy(P);                                //
 sm2.selfadjointView<Lower>() = A.selfadjointView<Lower>().twistedBy(P);       // compute P S P' from the lower triangular part of A, and then only compute the lower part
  \endcode
 
-\subsection TutorialSparse_Submat Sub-matrices
-
-%Sparse matrices does not support yet the addressing of arbitrary sub matrices. Currently, one can only reference a set of contiguous \em inner vectors, i.e., a set of contiguous rows for a row-major matrix, or a set of contiguous columns for a column major matrix:
-\code
-  sm1.innerVector(j);       // returns an expression of the j-th column (resp. row) of the matrix if sm1 is col-major (resp. row-major)
-  sm1.innerVectors(j, nb);  // returns an expression of the nb columns (resp. row) starting from the j-th column (resp. row)
-                            // of the matrix if sm1 is col-major (resp. row-major)
-  sm1.middleRows(j, nb);    // for row major matrices only, get a range of nb rows
-  sm1.middleCols(j, nb);    // for column major matrices only, get a range of nb columns
-\endcode
-
-\li \b Next: \ref TutorialMapClass
+Please, refer to the \link SparseQuickRefPage Quick Reference \endlink  guide for the list of supported operations. The list of linear solvers available is \link TopicSparseSystems here. \endlink
 
 */
 
diff --git a/doc/D11_UnalignedArrayAssert.dox b/doc/UnalignedArrayAssert.dox
index d173ee5f4..8c97d7874 100644
--- a/doc/D11_UnalignedArrayAssert.dox
+++ b/doc/UnalignedArrayAssert.dox
@@ -1,6 +1,6 @@
 namespace Eigen {
 
-/** \page TopicUnalignedArrayAssert Explanation of the assertion on unaligned arrays
+/** \eigenManualPage TopicUnalignedArrayAssert Explanation of the assertion on unaligned arrays
 
 Hello! You are seeing this webpage because your program terminated on an assertion failure like this one:
 <pre>
@@ -14,14 +14,7 @@ is explained here: http://eigen.tuxfamily.org/dox/UnalignedArrayAssert.html
 
 There are 4 known causes for this issue. Please read on to understand them and learn how to fix them.
 
-\b Table \b of \b contents
- - \ref where
- - \ref c1
- - \ref c2
- - \ref c3
- - \ref c4
- - \ref explanation
- - \ref getrid
+\eigenAutoToc
 
 \section where Where in my own code is the cause of the problem?
 
diff --git a/doc/UsingIntelMKL.dox b/doc/UsingIntelMKL.dox
index 379ee3ffd..4b624a156 100644
--- a/doc/UsingIntelMKL.dox
+++ b/doc/UsingIntelMKL.dox
@@ -40,7 +40,7 @@ Since Eigen version 3.1 and later, users can benefit from built-in Intel MKL opt
 <a href="http://eigen.tuxfamily.org/Counter/redirect_to_mkl.php"> Intel MKL </a> provides highly optimized multi-threaded mathematical routines for x86-compatible architectures.
 Intel MKL is available on Linux, Mac and Windows for both Intel64 and IA32 architectures.
 
-\warning Be aware that Intel® MKL is a proprietary software. It is the responsibility of the users to buy MKL licenses for their products. Moreover, the license of the user product has to allow linking to proprietary software that excludes any unmodified versions of the GPL. As a consequence, this also means that Eigen has to be used through the LGPL3+ license.
+\warning Be aware that Intel® MKL is a proprietary software. It is the responsibility of the users to buy MKL licenses for their products. Moreover, the license of the user product has to allow linking to proprietary software that excludes any unmodified versions of the GPL.
 
 Using Intel MKL through Eigen is easy:
 -# define the \c EIGEN_USE_MKL_ALL macro before including any Eigen's header
@@ -61,7 +61,7 @@ In addition you can coarsely select choose which parts will be substituted by de
 <tr><td>\c EIGEN_USE_MKL_ALL </td><td>Defines \c EIGEN_USE_BLAS, \c EIGEN_USE_LAPACKE, and \c EIGEN_USE_MKL_VML </td></tr>
 </table>
 
-Finally, the PARDISO sparse solver shipped with Intel MKL can be used through the \ref PardisoLU, \ref PardisoLLT and \ref PardisoLDLT classes of the \ref PARDISOSupport_Module.
+Finally, the PARDISO sparse solver shipped with Intel MKL can be used through the \ref PardisoLU, \ref PardisoLLT and \ref PardisoLDLT classes of the \ref PardisoSupport_Module.
 
 
 \section TopicUsingIntelMKL_SupportedFeatures List of supported features
@@ -165,4 +165,4 @@ In the examples, m1 and m2 are dense matrices and v1 and v2 are dense vectors.
 
 */
 
-}
\ No newline at end of file
+}
diff --git a/doc/D03_WrongStackAlignment.dox b/doc/WrongStackAlignment.dox
index b0e42edce..17d5513a7 100644
--- a/doc/D03_WrongStackAlignment.dox
+++ b/doc/WrongStackAlignment.dox
@@ -1,6 +1,6 @@
 namespace Eigen {
 
-/** \page TopicWrongStackAlignment Compiler making a wrong assumption on stack alignment
+/** \eigenManualPage TopicWrongStackAlignment Compiler making a wrong assumption on stack alignment
 
 <h4>It appears that this was a GCC bug that has been fixed in GCC 4.5.
 If you hit this issue, please upgrade to GCC 4.5 and report to us, so we can update this page.</h4>
diff --git a/doc/eigen_navtree_hacks.js b/doc/eigen_navtree_hacks.js
new file mode 100644
index 000000000..bd7e02b38
--- /dev/null
+++ b/doc/eigen_navtree_hacks.js
@@ -0,0 +1,240 @@
+
+// generate a table of contents in the side-nav based on the h1/h2 tags of the current page.
+function generate_autotoc() {
+  var headers = $("h1, h2");
+  if(headers.length > 1) {
+    var toc = $("#side-nav").append('<div id="nav-toc" class="toc"><h3>Table of contents</h3></div>');
+    toc = $("#nav-toc");
+    var footerHeight = footer.height();
+    toc = toc.append('<ul></ul>');
+    toc = toc.find('ul');
+    var indices = new Array();
+    indices[0] = 0;
+    indices[1] = 0;
+
+    var h1counts = $("h1").length;
+    headers.each(function(i) {
+      var current = $(this);
+      var levelTag = current[0].tagName.charAt(1);
+      if(h1counts==0)
+        levelTag--;
+      var cur_id = current.attr("id");
+
+      indices[levelTag-1]+=1;  
+      var prefix = indices[0];
+      if (levelTag >1) {
+        prefix+="."+indices[1];
+      }
+        
+      // Uncomment to add number prefixes
+      // current.html(prefix + "   " + current.html());
+      for(var l = levelTag; l < 2; ++l){
+          indices[l] = 0;
+      }
+
+      if(cur_id == undefined) {
+        current.attr('id', 'title' + i);
+        current.addClass('anchor');
+        toc.append("<li class='level" + levelTag + "'><a id='link" + i + "' href='#title" +
+                    i + "' title='" + current.prop("tagName") + "'>" + current.text() + "</a></li>");
+      } else {
+        toc.append("<li class='level" + levelTag + "'><a id='" + cur_id + "' href='#title" +
+                    i + "' title='" + current.prop("tagName") + "'>" + current.text() + "</a></li>");
+      }
+    });
+    resizeHeight();
+  }
+}
+
+
+var global_navtree_object;
+
+// Overloaded to remove links to sections/subsections
+function getNode(o, po)
+{
+  po.childrenVisited = true;
+  var l = po.childrenData.length-1;
+  for (var i in po.childrenData) {
+    var nodeData = po.childrenData[i];
+    if((!nodeData[1]) ||  (nodeData[1].indexOf('#')==-1)) // <- we added this line
+      po.children[i] = newNode(o, po, nodeData[0], nodeData[1], nodeData[2], i==l);
+  }
+}
+
+// Overloaded to adjust the size of the navtree wrt the toc
+function resizeHeight() 
+{
+  var toc = $("#nav-toc");
+  var tocHeight = toc.height();  // <- we added this line
+  var headerHeight = header.height();
+  var footerHeight = footer.height();
+  var windowHeight = $(window).height() - headerHeight - footerHeight;
+  content.css({height:windowHeight + "px"});
+  navtree.css({height:(windowHeight-tocHeight) + "px"}); // <- we modified this line
+  sidenav.css({height:(windowHeight) + "px",top: headerHeight+"px"});
+}
+
+// Overloaded to save the root node into global_navtree_object
+function initNavTree(toroot,relpath)
+{
+  var o = new Object();
+  global_navtree_object = o; // <- we added this line
+  o.toroot = toroot;
+  o.node = new Object();
+  o.node.li = document.getElementById("nav-tree-contents");
+  o.node.childrenData = NAVTREE;
+  o.node.children = new Array();
+  o.node.childrenUL = document.createElement("ul");
+  o.node.getChildrenUL = function() { return o.node.childrenUL; };
+  o.node.li.appendChild(o.node.childrenUL);
+  o.node.depth = 0;
+  o.node.relpath = relpath;
+  o.node.expanded = false;
+  o.node.isLast = true;
+  o.node.plus_img = document.createElement("img");
+  o.node.plus_img.src = relpath+"ftv2pnode.png";
+  o.node.plus_img.width = 16;
+  o.node.plus_img.height = 22;
+
+  if (localStorageSupported()) {
+    var navSync = $('#nav-sync');
+    if (cachedLink()) {
+      showSyncOff(navSync,relpath);
+      navSync.removeClass('sync');
+    } else {
+      showSyncOn(navSync,relpath);
+    }
+    navSync.click(function(){ toggleSyncButton(relpath); });
+  }
+
+  navTo(o,toroot,window.location.hash,relpath);
+
+  $(window).bind('hashchange', function(){
+     if (window.location.hash && window.location.hash.length>1){
+       var a;
+       if ($(location).attr('hash')){
+         var clslink=stripPath($(location).attr('pathname'))+':'+
+                               $(location).attr('hash').substring(1);
+         a=$('.item a[class$="'+clslink+'"]');
+       }
+       if (a==null || !$(a).parent().parent().hasClass('selected')){
+         $('.item').removeClass('selected');
+         $('.item').removeAttr('id');
+       }
+       var link=stripPath2($(location).attr('pathname'));
+       navTo(o,link,$(location).attr('hash'),relpath);
+     } else if (!animationInProgress) {
+       $('#doc-content').scrollTop(0);
+       $('.item').removeClass('selected');
+       $('.item').removeAttr('id');
+       navTo(o,toroot,window.location.hash,relpath);
+     }
+  })
+
+  $(window).load(showRoot);
+}
+
+// return false if the the node has no children at all, or has only section/subsection children
+function checkChildrenData(node) {
+  if (!(typeof(node.childrenData)==='string')) {
+    for (var i in node.childrenData) {
+      var url = node.childrenData[i][1];
+      if(url.indexOf("#")==-1)
+        return true;
+    }
+    return false;
+  }
+  return (node.childrenData);
+}
+
+// Modified to:
+// 1 - remove the root node 
+// 2 - remove the section/subsection children
+function createIndent(o,domNode,node,level)
+{
+  var level=-2; // <- we replaced level=-1 by level=-2
+  var n = node;
+  while (n.parentNode) { level++; n=n.parentNode; }
+  var imgNode = document.createElement("img");
+  imgNode.style.paddingLeft=(16*(level)).toString()+'px';
+  imgNode.width  = 16;
+  imgNode.height = 22;
+  imgNode.border = 0;
+  if (checkChildrenData(node)) { // <- we modified this line to use checkChildrenData(node) instead of node.childrenData
+    node.plus_img = imgNode;
+    node.expandToggle = document.createElement("a");
+    node.expandToggle.href = "javascript:void(0)";
+    node.expandToggle.onclick = function() {
+      if (node.expanded) {
+        $(node.getChildrenUL()).slideUp("fast");
+        node.plus_img.src = node.relpath+"ftv2pnode.png";
+        node.expanded = false;
+      } else {
+        expandNode(o, node, false, false);
+      }
+    }
+    node.expandToggle.appendChild(imgNode);
+    domNode.appendChild(node.expandToggle);
+    imgNode.src = node.relpath+"ftv2pnode.png";
+  } else {
+    imgNode.src = node.relpath+"ftv2node.png";
+    domNode.appendChild(imgNode);
+  } 
+}
+
+// Overloaded to automatically expand the selected node
+function selectAndHighlight(hash,n)
+{
+  var a;
+  if (hash) {
+    var link=stripPath($(location).attr('pathname'))+':'+hash.substring(1);
+    a=$('.item a[class$="'+link+'"]');
+  }
+  if (a && a.length) {
+    a.parent().parent().addClass('selected');
+    a.parent().parent().attr('id','selected');
+    highlightAnchor();
+  } else if (n) {
+    $(n.itemDiv).addClass('selected');
+    $(n.itemDiv).attr('id','selected');
+  }
+  if ($('#nav-tree-contents .item:first').hasClass('selected')) {
+    $('#nav-sync').css('top','30px');
+  } else {
+    $('#nav-sync').css('top','5px');
+  }
+  expandNode(global_navtree_object, n, true, true); // <- we added this line
+  showRoot();
+}
+
+
+$(document).ready(function() {
+  
+  generate_autotoc();
+  
+  (function (){ // wait until the first "selected" element has been created
+    try {
+      
+      // this line will triger an exception if there is no #selected element, i.e., before the tree structure is complete.
+      document.getElementById("selected").className = "item selected";
+      
+      // ok, the default tree has been created, we can keep going...
+      
+      // expand the "Chapters" node
+      if(window.location.href.indexOf('unsupported')==-1)
+        expandNode(global_navtree_object, global_navtree_object.node.children[0].children[2], true, true);
+      else
+        expandNode(global_navtree_object, global_navtree_object.node.children[0].children[1], true, true);
+      
+      // Hide the root node "Eigen"
+      $(document.getElementsByClassName('index.html')[0]).parent().parent().css({display:"none"});
+      
+    } catch (err) {
+      setTimeout(arguments.callee, 10);
+    }
+  })();
+});
+
+$(window).load(function() {
+  resizeHeight();
+});
diff --git a/doc/eigendoxy.css b/doc/eigendoxy.css
index c6c16286d..efaeb46dc 100644
--- a/doc/eigendoxy.css
+++ b/doc/eigendoxy.css
@@ -1,708 +1,33 @@
-/* The standard CSS for doxygen */
 
-body, table, div, p, dl {
-  font-family: Lucida Grande, Verdana, Geneva, Arial, sans-serif;
-  font-size: 12px;
-}
-
-/* @group Heading Levels */
-
-h1 {
-  font-size: 150%;
-}
-
-h2 {
-  font-size: 120%;
-}
-
-h3 {
-  font-size: 100%;
-}
-
-dt {
-  font-weight: bold;
-}
-
-div.multicol {
-  -moz-column-gap: 1em;
-  -webkit-column-gap: 1em;
-  -moz-column-count: 3;
-  -webkit-column-count: 3;
-}
-
-p.startli, p.startdd, p.starttd {
-  margin-top: 2px;
-}
-
-p.endli {
-  margin-bottom: 0px;
-}
-
-p.enddd {
-  margin-bottom: 4px;
-}
-
-p.endtd {
-  margin-bottom: 2px;
-}
-
-/* @end */
-
-caption {
-  font-weight: bold;
-}
-
-span.legend {
-        font-size: 70%;
-        text-align: center;
-}
-
-h3.version {
-        font-size: 90%;
-        text-align: center;
-}
-
-div.qindex, div.navtab{
-  background-color: #EBEFF6;
-  border: 1px solid #A3B4D7;
-  text-align: center;
-  margin: 2px;
-  padding: 2px;
-}
-
-div.qindex, div.navpath {
-  width: 100%;
-  line-height: 140%;
-}
-
-div.navtab {
-  margin-right: 15px;
-}
-
-/* @group Link Styling */
-
-a {
-  color: #3D578C;
-  font-weight: normal;
-  text-decoration: none;
-}
-
-.contents a:visited {
-  color: #4665A2;
-}
-
-a:hover {
-  text-decoration: underline;
-}
-
-a.qindex {
-  font-weight: bold;
-}
-
-a.qindexHL {
-  font-weight: bold;
-  background-color: #9CAFD4;
-  color: #ffffff;
-  border: 1px double #869DCA;
-}
-
-.contents a.qindexHL:visited {
-        color: #ffffff;
-}
-
-a.el {
-  font-weight: bold;
-}
-
-a.elRef {
-}
-
-a.code {
-  color: #4665A2;
-}
-
-a.codeRef {
-  color: #4665A2;
-}
-
-/* @end */
-
-dl.el {
-  margin-left: -1cm;
-}
-
-.fragment {
-  font-family: monospace, fixed;
-  font-size: 105%;
-}
-
-pre.fragment {
-  border: 1px solid #C4CFE5;
-  background-color: #FBFCFD;
-  padding: 4px 6px;
-  margin: 4px 8px 4px 2px;
-  overflow: auto;
-  /*word-wrap: break-word;*/
-  font-size:  9pt;
-  line-height: 125%;
-}
-
-div.ah {
-  background-color: black;
-  font-weight: bold;
-  color: #ffffff;
-  margin-bottom: 3px;
-  margin-top: 3px;
-  padding: 0.2em;
-  border: solid thin #333;
-  border-radius: 0.5em;
-  -webkit-border-radius: .5em;
-  -moz-border-radius: .5em;
-  box-shadow: 2px 2px 3px #999;
-  -webkit-box-shadow: 2px 2px 3px #999;
-  -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
-  background-image: -webkit-gradient(linear, left top, left bottom, from(#eee), to(#000),color-stop(0.3, #444));
-  background-image: -moz-linear-gradient(center top, #eee 0%, #444 40%, #000);
-}
-
-div.groupHeader {
-  margin-left: 16px;
-  margin-top: 12px;
-  font-weight: bold;
-}
-
-div.groupText {
-  margin-left: 16px;
-  font-style: italic;
-}
-
-body {
-  background: white;
-  color: black;
-        margin: 0;
-}
-
-div.contents {
-  margin-top: 10px;
-  margin-left: 10px;
-  margin-right: 10px;
-}
-
-td.indexkey {
-  background-color: #EBEFF6;
-  font-weight: bold;
-  border: 1px solid #C4CFE5;
-  margin: 2px 0px 2px 0;
-  padding: 2px 10px;
-}
-
-td.indexvalue {
-  background-color: #EBEFF6;
-  border: 1px solid #C4CFE5;
-  padding: 2px 10px;
-  margin: 2px 0px;
-}
-
-tr.memlist {
-  background-color: #EEF1F7;
-}
-
-p.formulaDsp {
-  text-align: center;
-}
-
-img.formulaDsp {
-  
-}
-
-img.formulaInl {
-  vertical-align: middle;
-}
-
-div.center {
-  text-align: center;
-        margin-top: 0px;
-        margin-bottom: 0px;
-        padding: 0px;
-}
-
-div.center img {
-  border: 0px;
-}
-
-address.footer {
-  text-align: right;
-  padding-right: 12px;
-}
-
-img.footer {
-  border: 0px;
-  vertical-align: middle;
-}
-
-/* @group Code Colorization */
-
-span.keyword {
-  color: #008000
-}
-
-span.keywordtype {
-  color: #604020
-}
-
-span.keywordflow {
-  color: #e08000
-}
-
-span.comment {
-  color: #800000
-}
-
-span.preprocessor {
-  color: #806020
-}
-
-span.stringliteral {
-  color: #002080
-}
-
-span.charliteral {
-  color: #008080
-}
-
-span.vhdldigit { 
-  color: #ff00ff 
-}
-
-span.vhdlchar { 
-  color: #000000 
-}
-
-span.vhdlkeyword { 
-  color: #700070 
-}
-
-span.vhdllogic { 
-  color: #ff0000 
-}
-
-/* @end */
-
-/*
-.search {
-  color: #003399;
-  font-weight: bold;
-}
-
-form.search {
-  margin-bottom: 0px;
-  margin-top: 0px;
-}
-
-input.search {
-  font-size: 75%;
-  color: #000080;
-  font-weight: normal;
-  background-color: #e8eef2;
-}
-*/
-
-td.tiny {
-  font-size: 75%;
-}
-
-.dirtab {
-  padding: 4px;
-  border-collapse: collapse;
-  border: 1px solid #A3B4D7;
-}
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-th.dirtab {
-  background: #EBEFF6;
-  font-weight: bold;
-}
-
-hr {
-  height: 0px;
-  border: none;
-  border-top: 1px solid #4A6AAA;
-}
-
-hr.footer {
-  height: 1px;
-}
-
-/* @group Member Descriptions */
-
-table.memberdecls {
-  border-spacing: 0px;
-  padding: 0px;
-}
-
-.mdescLeft, .mdescRight,
-.memItemLeft, .memItemRight,
-.memTemplItemLeft, .memTemplItemRight, .memTemplParams {
-  background-color: #F9FAFC;
-  border: none;
-  margin: 4px;
-  padding: 1px 0 0 8px;
-}
-
-.mdescLeft, .mdescRight {
-  padding: 0px 8px 4px 8px;
-  color: #555;
-}
-
-.memItemLeft, .memItemRight, .memTemplParams {
-  border-top: 1px solid #C4CFE5;
-}
-
-.memItemLeft, .memTemplItemLeft {
-        white-space: nowrap;
-}
-
-.memTemplParams {
-  color: #4665A2;
-        white-space: nowrap;
-}
-
-/* @end */
-
-/* @group Member Details */
-
-/* Styles for detailed member documentation */
-
-.memtemplate {
-  font-size: 80%;
-  color: #4665A2;
-  font-weight: normal;
-  margin-left: 9px;
-}
-
-.memnav {
-  background-color: #EBEFF6;
-  border: 1px solid #A3B4D7;
-  text-align: center;
-  margin: 2px;
-  margin-right: 15px;
-  padding: 2px;
-}
-
-.memitem {
-  padding: 0;
-  margin-bottom: 10px;
-}
-
-.memname {
-        white-space: nowrap;
-        font-weight: bold;
-        margin-left: 6px;
-}
-
-.memproto {
-        border-top: 1px solid #A8B8D9;
-        border-left: 1px solid #A8B8D9;
-        border-right: 1px solid #A8B8D9;
-        padding: 6px 0px 6px 0px;
-        color: #253555;
-        font-weight: bold;
-        text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
-        /* opera specific markup */
-        box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
-        border-top-right-radius: 8px;
-        border-top-left-radius: 8px;
-        /* firefox specific markup */
-        -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
-        -moz-border-radius-topright: 8px;
-        -moz-border-radius-topleft: 8px;
-        /* webkit specific markup */
-        -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
-        -webkit-border-top-right-radius: 8px;
-        -webkit-border-top-left-radius: 8px;
-        background-image:url('nav_f.png');
-        background-repeat:repeat-x;
-        background-color: #E2E8F2;
-
-}
-
-.memdoc {
-        border-bottom: 1px solid #A8B8D9;      
-        border-left: 1px solid #A8B8D9;      
-        border-right: 1px solid #A8B8D9; 
-        padding: 2px 5px;
-        background-color: #FBFCFD;
-        border-top-width: 0;
-        /* opera specific markup */
-        border-bottom-left-radius: 8px;
-        border-bottom-right-radius: 8px;
-        box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
-        /* firefox specific markup */
-        -moz-border-radius-bottomleft: 8px;
-        -moz-border-radius-bottomright: 8px;
-        -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
-        background-image: -moz-linear-gradient(center top, #FFFFFF 0%, #FFFFFF 60%, #F7F8FB 95%, #EEF1F7);
-        /* webkit specific markup */
-        -webkit-border-bottom-left-radius: 8px;
-        -webkit-border-bottom-right-radius: 8px;
-        -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
-        background-image: -webkit-gradient(linear,center top,center bottom,from(#FFFFFF), color-stop(0.6,#FFFFFF), color-stop(0.60,#FFFFFF), color-stop(0.95,#F7F8FB), to(#EEF1F7));
-}
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-.params .paramdir {
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-
-
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-
-/* @group Directory (tree) */
-
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-
-.ftvtree {
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-  margin: 0px;
-}
-
-/* these are for tree view when used as main index */
-
-.directory {
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-.directory h3 {
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-  margin-top: 1em;
-  font-size: 11pt;
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-
-/*
-The following two styles can be used to replace the root node title
-with an image of your choice.  Simply uncomment the next two styles,
-specify the name of your image and be sure to set 'height' to the
-proper pixel height of your image.
-*/
-
-/*
-.directory h3.swap {
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-.directory h3.swap span {
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-.directory img {
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-}
-
-.directory-alt p {
-  margin: 0px;
-  white-space: nowrap;
-}
-
-.directory-alt div {
-  display: none;
-  margin: 0px;
-}
-
-.directory-alt img {
-  vertical-align: -30%;
-}
-
-/* @end */
-
-div.dynheader {
-        margin-top: 8px;
-}
-
-address {
-  font-style: normal;
-  color: #2A3D61;
-}
-
-table.doxtable {
-  border-collapse:collapse;
-}
-
-table.doxtable td, table.doxtable th {
-  border: 1px solid #2D4068;
-  padding: 3px 7px 2px;
-}
-
-table.doxtable th {
-  background-color: #374F7F;
-  color: #FFFFFF;
-  font-size: 110%;
-  padding-bottom: 4px;
-  padding-top: 5px;
-  text-align:left;
-}
-
-.tabsearch {
-  top: 0px;
-  left: 10px;
-  height: 36px;
-  background-image: url('tab_b.png');
-  z-index: 101;
-  overflow: hidden;
-  font-size: 13px;
-}
-
-.navpath ul
-{
-  font-size: 11px;
-  background-image:url('tab_b.png');
-  background-repeat:repeat-x;
-  height:30px;
-  line-height:30px;
-  color:#8AA0CC;
-  border:solid 1px #C2CDE4;
-  overflow:hidden;
-  margin:0px;
-  padding:0px;
-}
-
-.navpath li
-{
-  list-style-type:none;
-  float:left;
-  padding-left:10px;
-  padding-right: 15px;
-  background-image:url('bc_s.png');
-  background-repeat:no-repeat;
-  background-position:right;
-  color:#364D7C;
-}
+/******** Eigen specific CSS code ************/
 
-.navpath a
-{
-  height:32px;
-  display:block;
-  text-decoration: none;
-  outline: none;
-}
+/**** Styles removing elements ****/
 
-.navpath a:hover
-{
-  color:#6884BD;
+/* remove the "modules|classes" link for module pages (they are already in the TOC) */
+div.summary {
+  display:none;
 }
 
-div.summary
-{
-  float: right;
-  font-size: 8pt;
-  padding-right: 5px;
-  width: 50%;
-  text-align: right;
-}       
-
-div.summary a
-{
-  white-space: nowrap;
+/* remove */
+div.contents hr {
+  display:none;
 }
 
-div.header
-{
-        background-image:url('nav_h.png');
-        background-repeat:repeat-x;
-  background-color: #F9FAFC;
-  margin:  0px;
-  border-bottom: 1px solid #C4CFE5;
-}
+/**** ****/
 
-div.headertitle
+p, dl.warning, dl.attention, dl.note
 {
-  padding: 5px 5px 5px 10px;
-}
-
-
-
-/******** Eigen specific CSS code ************/
-
-
-body {
   max-width:60em;
-  margin-left:5%;
-  margin-top:2%;
-  font-family: Lucida Grande, Verdana, Geneva, Arial, sans-serif;
+  text-align:justify;
 }
 
-img {
-    border: 0;
+li {
+  max-width:55em;
+  text-align:justify;  
 }
 
-a.logo {
-  float:right;
-  margin:10px;
+img {
+  border: 0;
 }
 
 div.fragment {
@@ -712,10 +37,12 @@ div.fragment {
 pre.fragment {
   border: 1px solid #cccccc;
 
-  margin: 2px 0px 2px 0px ;
+  margin: 2px 0px 2px 0px;
   padding: 3px 5px 3px 5px;
 }
 
+
+
 /* Common style for all Eigen's tables */
 
 table.example, table.manual, table.manual-vl {
@@ -816,51 +143,31 @@ h2 {
   border-color: #cccccc;
 }
 
+/**** Table of content in the side-nav ****/
 
-/**** old Eigen's styles ****/
 
-th {
-    /*text-align: left;
-    padding-right: 1em;*/
-    /* border: #cccccc dashed; */
-    /* border-style: dashed; */
-    /* border-width: 0 0 3px 0; */
-}
-/*
-table.noborder {
-  border-collapse: separate;
-  border-bottom-style : none;
-  border-left-style   : none;
-  border-right-style  : none;
-  border-top-style : none ;
-  border-spacing : 0px 0px;
-  margin: 4pt 0 0 0;
-  padding: 0 0 0 0;
-  
-    -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
-    -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+div.toc {
+  margin:0;
+  padding: 0.3em 0 0 0;
+  width:100%;
+  float:none;
+  position:absolute;
+  bottom:0;
+  border-radius:0px;
+  border-style: solid none none none;
 }
 
-table.noborder td {
-  border-bottom-style : none;
-  border-left-style   : none;
-  border-right-style  : none;
-  border-top-style : none;
-  border-spacing : 0px 0px;
-  margin: 0 0 0 0;
-  vertical-align: top;
+div.toc h3 {
+  margin-left: 0.5em;
+  margin-bottom: 0.2em;
 }
 
-table.tutorial_code {
-  width: 90%;
-    -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
-    -moz-box-shadow: rgba(0, 0, 0, 0.15) 5px 5px 5px;
+div.toc ul {
+  margin: 0.2em 0 0.4em 0.5em;
 }
 
-table.tutorial_code tr {
-  border: 1px dashed #888888;
-}
-*/
+/**** old Eigen's styles ****/
+
 
 table.tutorial_code td {
   border-color: transparent; /* required for Firefox */
@@ -878,23 +185,6 @@ table.tutorial_code td.note p.starttd {
   border: none;
   padding: 0px;
 }
-/*
-div.fragment {
-  font-family: monospace, fixed;
-  font-size: 95%;
-  
-  border: none;
-  padding: 0pt;
-}
-
-pre.fragment {
-  margin: 0pt;
-  border: 1px solid #cccccc;
-  padding: 2px 5px 2px 5px;
-  
-  background-color: #f5f5f5;
-}
-*/
 
 div.eimainmenu {
   text-align:     center;
@@ -909,3 +199,13 @@ h3.version {
 td.width20em p.endtd {
   width:  20em;
 }
+
+.bigwarning {
+  font-size:2em;
+  font-weight:bold;
+  margin:1em;
+  padding:1em;
+  color:red;
+  border:solid;
+}
+
diff --git a/doc/eigendoxy_footer.html.in b/doc/eigendoxy_footer.html.in
index e70829fb0..878244a19 100644
--- a/doc/eigendoxy_footer.html.in
+++ b/doc/eigendoxy_footer.html.in
@@ -1,5 +1,36 @@
-
+<!-- start footer part -->
+<!--BEGIN GENERATE_TREEVIEW-->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    $navpath
+    <li class="footer">$generatedby
+    <a href="http://www.doxygen.org/index.html">
+    <img class="footer" src="$relpath$doxygen.png" alt="doxygen"/></a> $doxygenversion </li>
+  </ul>
+</div>
+<!--END GENERATE_TREEVIEW-->
+<!--BEGIN !GENERATE_TREEVIEW-->
 <hr class="footer"/><address class="footer"><small>
-<a href="http://www.doxygen.org/index.html"><img class="footer" src="$relpath$doxygen.png" alt="doxygen"/></a></small></address>
+$generatedby &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="$relpath$doxygen.png" alt="doxygen"/>
+</a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+
+<!-- Piwik -->
+<script type="text/javascript">
+var pkBaseURL = (("https:" == document.location.protocol) ? "https://stats.sylphide-consulting.com/piwik/" : "http://stats.sylphide-consulting.com/piwik/");
+document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E"));
+</script><script type="text/javascript">
+try {
+var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", 20);
+piwikTracker.trackPageView();
+piwikTracker.enableLinkTracking();
+} catch( err ) {}
+</script><noscript><p><img src="http://stats.sylphide-consulting.com/piwik/piwik.php?idsite=20" style="border:0" alt="" /></p></noscript>
+<!-- End Piwik Tracking Code -->
+
 </body>
-</html>
\ No newline at end of file
+</html>
+
+
diff --git a/doc/eigendoxy_header.html.in b/doc/eigendoxy_header.html.in
index a4fe47f27..0f3859f40 100644
--- a/doc/eigendoxy_header.html.in
+++ b/doc/eigendoxy_header.html.in
@@ -2,13 +2,60 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
 <head>
 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
-<title>$title</title>
-<link href="$relpath$eigendoxy_tabs.css" rel="stylesheet" type="text/css">
-<link href="$relpath$search/search.css" rel="stylesheet" type="text/css"/>
-<script type="text/javaScript" src="$relpath$search/search.js"></script>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen $doxygenversion"/>
+<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+<link href="$relpath$tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="$relpath$jquery.js"></script>
+<script type="text/javascript" src="$relpath$dynsections.js"></script>
+$treeview
+$search
+$mathjax
+<link href="$relpath$$stylesheet"   rel="stylesheet" type="text/css" />
 <link href="$relpath$eigendoxy.css" rel="stylesheet" type="text/css">
+<!-- $extrastylesheet -->
+<script type="text/javascript" src="$relpath$eigen_navtree_hacks.js"></script>
+<!-- <script type="text/javascript"> -->
+<!-- </script> -->
+
 </head>
-<body onload='searchBox.OnSelectItem(0);'>
-<a name="top"></a>
-<a class="logo" href="http://eigen.tuxfamily.org/">
-<img class="logo" src="Eigen_Silly_Professor_64x64.png" width=64 height=64 alt="Eigen's silly professor"/></a>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<!-- <a name="top"></a> -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+  <!--BEGIN PROJECT_LOGO-->
+  <td id="projectlogo"><img alt="Logo" src="$relpath$$projectlogo"/></td>
+  <!--END PROJECT_LOGO-->
+  <!--BEGIN PROJECT_NAME-->
+  <td style="padding-left: 0.5em;">
+   <div id="projectname"><a href="http://eigen.tuxfamily.org">$projectname</a>
+   <!--BEGIN PROJECT_NUMBER-->&#160;<span id="projectnumber">$projectnumber</span><!--END PROJECT_NUMBER-->
+   </div>
+   <!--BEGIN PROJECT_BRIEF--><div id="projectbrief">$projectbrief</div><!--END PROJECT_BRIEF-->
+  </td>
+  <!--END PROJECT_NAME-->
+  <!--BEGIN !PROJECT_NAME-->
+   <!--BEGIN PROJECT_BRIEF-->
+    <td style="padding-left: 0.5em;">
+    <div id="projectbrief">$projectbrief</div>
+    </td>
+   <!--END PROJECT_BRIEF-->
+  <!--END !PROJECT_NAME-->
+  <!--BEGIN DISABLE_INDEX-->
+   <!--BEGIN SEARCHENGINE-->
+   <td>$searchbox</td>
+   <!--END SEARCHENGINE-->
+  <!--END DISABLE_INDEX-->
+ </tr>
+ </tbody>
+</table>
+</div>
+<!--END TITLEAREA-->
+<!-- end header part -->
+
diff --git a/doc/eigendoxy_layout.xml.in b/doc/eigendoxy_layout.xml.in
new file mode 100644
index 000000000..c14b621e5
--- /dev/null
+++ b/doc/eigendoxy_layout.xml.in
@@ -0,0 +1,178 @@
+<?xml version="1.0"?>
+<doxygenlayout version="1.0">
+  <!-- Navigation index tabs for HTML output -->
+  <navindex>
+    <tab type="user" url="index.html" title="Overview" />
+    <tab type="user" url="@ref GettingStarted" title="Getting started" />
+    <tab type="modules" visible="yes" title="Chapters" intro=""/>
+    <tab type="mainpage" visible="yes" title=""/>
+    <tab type="classlist" visible="yes" title="" intro=""/>
+<!--     <tab type="classmembers" visible="yes" title="" intro=""/> -->
+  </navindex>
+
+  <!-- Layout definition for a class page -->
+  <class>
+    <briefdescription visible="no"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <detaileddescription title=""/>
+    <inheritancegraph visible="$CLASS_GRAPH"/>
+    <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+    <allmemberslink visible="yes"/>
+    <memberdecl>
+      <nestedclasses visible="yes" title=""/>
+      <publictypes title=""/>
+      <publicslots title=""/>
+      <signals title=""/>
+      <publicmethods title=""/>
+      <publicstaticmethods title=""/>
+      <publicattributes title=""/>
+      <publicstaticattributes title=""/>
+      <protectedtypes title=""/>
+      <protectedslots title=""/>
+      <protectedmethods title=""/>
+      <protectedstaticmethods title=""/>
+      <protectedattributes title=""/>
+      <protectedstaticattributes title=""/>
+      <packagetypes title=""/>
+      <packagemethods title=""/>
+      <packagestaticmethods title=""/>
+      <packageattributes title=""/>
+      <packagestaticattributes title=""/>
+      <properties title=""/>
+      <events title=""/>
+      <privatetypes title=""/>
+      <privateslots title=""/>
+      <privatemethods title=""/>
+      <privatestaticmethods title=""/>
+      <privateattributes title=""/>
+      <privatestaticattributes title=""/>
+      <friends title=""/>
+      <related title="" subtitle=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <constructors title=""/>
+      <functions title=""/>
+      <related title=""/>
+      <variables title=""/>
+      <properties title=""/>
+      <events title=""/>
+    </memberdef>
+    <usedfiles visible="$SHOW_USED_FILES"/>
+    <authorsection visible="yes"/>
+  </class>
+
+  <!-- Layout definition for a namespace page -->
+  <namespace>
+    <briefdescription visible="yes"/>
+    <memberdecl>
+      <nestednamespaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </namespace>
+
+  <!-- Layout definition for a file page -->
+  <file>
+    <briefdescription visible="yes"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <includegraph visible="$INCLUDE_GRAPH"/>
+    <includedbygraph visible="$INCLUDED_BY_GRAPH"/>
+    <sourcelink visible="yes"/>
+    <memberdecl>
+      <classes visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection/>
+  </file>
+
+  <!-- Layout definition for a group page -->
+  <group>
+    <briefdescription visible="no"/>
+    <detaileddescription title=""/>
+    <groupgraph visible="$GROUP_GRAPHS"/>
+    <memberdecl>
+      <nestedgroups visible="yes" title=""/>
+      <dirs visible="yes" title=""/>
+      <files visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    
+    <memberdef>
+      <pagedocs/>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </group>
+
+  <!-- Layout definition for a directory page -->
+  <directory>
+    <briefdescription visible="yes"/>
+    <directorygraph visible="yes"/>
+    <memberdecl>
+      <dirs visible="yes"/>
+      <files visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+  </directory>
+</doxygenlayout>
diff --git a/doc/examples/CMakeLists.txt b/doc/examples/CMakeLists.txt
index 13ec0c123..71b272a15 100644
--- a/doc/examples/CMakeLists.txt
+++ b/doc/examples/CMakeLists.txt
@@ -1,7 +1,5 @@
 file(GLOB examples_SRCS "*.cpp")
 
-add_custom_target(all_examples)
-
 foreach(example_src ${examples_SRCS})
   get_filename_component(example ${example_src} NAME_WE)
   add_executable(${example} ${example_src})
diff --git a/doc/examples/QuickStart_example2_dynamic.cpp b/doc/examples/QuickStart_example2_dynamic.cpp
index 672ac82e9..ff6746e21 100644
--- a/doc/examples/QuickStart_example2_dynamic.cpp
+++ b/doc/examples/QuickStart_example2_dynamic.cpp
@@ -6,10 +6,10 @@ using namespace std;
 
 int main()
 {
-  MatrixXf m = MatrixXf::Random(3,3);
-  m = (m + MatrixXf::Constant(3,3,1.2)) * 50;
+  MatrixXd m = MatrixXd::Random(3,3);
+  m = (m + MatrixXd::Constant(3,3,1.2)) * 50;
   cout << "m =" << endl << m << endl;
-  VectorXf v(3);
+  VectorXd v(3);
   v << 1, 2, 3;
   cout << "m * v =" << endl << m * v << endl;
 }
diff --git a/doc/examples/QuickStart_example2_fixed.cpp b/doc/examples/QuickStart_example2_fixed.cpp
index edf3268cd..d91175273 100644
--- a/doc/examples/QuickStart_example2_fixed.cpp
+++ b/doc/examples/QuickStart_example2_fixed.cpp
@@ -6,10 +6,10 @@ using namespace std;
 
 int main()
 {
-  Matrix3f m = Matrix3f::Random();
-  m = (m + Matrix3f::Constant(1.2)) * 50;
+  Matrix3d m = Matrix3d::Random();
+  m = (m + Matrix3d::Constant(1.2)) * 50;
   cout << "m =" << endl << m << endl;
-  Vector3f v(1,2,3);
+  Vector3d v(1,2,3);
   
   cout << "m * v =" << endl << m * v << endl;
 }
diff --git a/doc/examples/function_taking_ref.cpp b/doc/examples/function_taking_ref.cpp
new file mode 100644
index 000000000..162a202e4
--- /dev/null
+++ b/doc/examples/function_taking_ref.cpp
@@ -0,0 +1,19 @@
+#include <iostream>
+#include <Eigen/SVD>
+using namespace Eigen;
+using namespace std;
+
+float inv_cond(const Ref<const MatrixXf>& a)
+{
+  const VectorXf sing_vals = a.jacobiSvd().singularValues();
+  return sing_vals(sing_vals.size()-1) / sing_vals(0);
+}
+
+int main()
+{
+  Matrix4f m = Matrix4f::Random();
+  cout << "matrix m:" << endl << m << endl << endl;
+  cout << "inv_cond(m):          " << inv_cond(m)                      << endl;
+  cout << "inv_cond(m(1:3,1:3)): " << inv_cond(m.topLeftCorner(3,3))   << endl;
+  cout << "inv_cond(m+I):        " << inv_cond(m+Matrix4f::Identity()) << endl;
+}
diff --git a/doc/snippets/Cwise_asin.cpp b/doc/snippets/Cwise_asin.cpp
new file mode 100644
index 000000000..8dad838fd
--- /dev/null
+++ b/doc/snippets/Cwise_asin.cpp
@@ -0,0 +1,2 @@
+Array3d v(0, sqrt(2.)/2, 1);
+cout << v.asin() << endl;
diff --git a/doc/snippets/DenseBase_setLinSpaced.cpp b/doc/snippets/DenseBase_setLinSpaced.cpp
index 50871dfcc..46054f234 100644
--- a/doc/snippets/DenseBase_setLinSpaced.cpp
+++ b/doc/snippets/DenseBase_setLinSpaced.cpp
@@ -1,3 +1,3 @@
 VectorXf v;
-v.setLinSpaced(5,0.5f,1.5f).transpose();
+v.setLinSpaced(5,0.5f,1.5f);
 cout << v << endl;
diff --git a/doc/snippets/GeneralizedEigenSolver.cpp b/doc/snippets/GeneralizedEigenSolver.cpp
new file mode 100644
index 000000000..2acda45fa
--- /dev/null
+++ b/doc/snippets/GeneralizedEigenSolver.cpp
@@ -0,0 +1,7 @@
+GeneralizedEigenSolver<MatrixXf> ges;
+MatrixXf A = MatrixXf::Random(4,4);
+MatrixXf B = MatrixXf::Random(4,4);
+ges.compute(A, B);
+cout << "The (complex) numerators of the generalzied eigenvalues are: " << ges.alphas().transpose() << endl;
+cout << "The (real) denominatore of the generalzied eigenvalues are: " << ges.betas().transpose() << endl;
+cout << "The (complex) generalzied eigenvalues are (alphas./beta): " << ges.eigenvalues().transpose() << endl;
diff --git a/doc/snippets/HouseholderQR_householderQ.cpp b/doc/snippets/HouseholderQR_householderQ.cpp
new file mode 100644
index 000000000..e859ce55b
--- /dev/null
+++ b/doc/snippets/HouseholderQR_householderQ.cpp
@@ -0,0 +1,7 @@
+MatrixXf A(MatrixXf::Random(5,3)), thinQ(MatrixXf::Identity(5,3)), Q;
+A.setRandom();
+HouseholderQR<MatrixXf> qr(A);
+Q = qr.householderQ();
+thinQ = qr.householderQ() * thinQ;
+std::cout << "The complete unitary matrix Q is:\n" << Q << "\n\n";
+std::cout << "The thin matrix Q is:\n" << thinQ << "\n\n";
diff --git a/doc/snippets/MatrixBase_applyOnTheLeft.cpp b/doc/snippets/MatrixBase_applyOnTheLeft.cpp
new file mode 100644
index 000000000..6398c873a
--- /dev/null
+++ b/doc/snippets/MatrixBase_applyOnTheLeft.cpp
@@ -0,0 +1,7 @@
+Matrix3f A = Matrix3f::Random(3,3), B;
+B << 0,1,0,  
+     0,0,1,  
+     1,0,0;
+cout << "At start, A = " << endl << A << endl;
+A.applyOnTheLeft(B); 
+cout << "After applyOnTheLeft, A = " << endl << A << endl;
diff --git a/doc/snippets/MatrixBase_applyOnTheRight.cpp b/doc/snippets/MatrixBase_applyOnTheRight.cpp
new file mode 100644
index 000000000..e4b71b2d8
--- /dev/null
+++ b/doc/snippets/MatrixBase_applyOnTheRight.cpp
@@ -0,0 +1,9 @@
+Matrix3f A = Matrix3f::Random(3,3), B;
+B << 0,1,0,  
+     0,0,1,  
+     1,0,0;
+cout << "At start, A = " << endl << A << endl;
+A *= B;
+cout << "After A *= B, A = " << endl << A << endl;
+A.applyOnTheRight(B);  // equivalent to A *= B
+cout << "After applyOnTheRight, A = " << endl << A << endl;
diff --git a/doc/snippets/MatrixBase_template_int_int_block_int_int_int_int.cpp b/doc/snippets/MatrixBase_template_int_int_block_int_int_int_int.cpp
new file mode 100644
index 000000000..4dced03ba
--- /dev/null
+++ b/doc/snippets/MatrixBase_template_int_int_block_int_int_int_int.cpp
@@ -0,0 +1,5 @@
+Matrix4i m = Matrix4i::Random();
+cout << "Here is the matrix m:" << endl << m << endl;
+cout << "Here is the block:" << endl << m.block<2, Dynamic>(1, 1, 2, 3) << endl;
+m.block<2, Dynamic>(1, 1, 2, 3).setZero();
+cout << "Now the matrix m is:" << endl << m << endl;
diff --git a/doc/snippets/MatrixBase_template_int_int_bottomLeftCorner_int_int.cpp b/doc/snippets/MatrixBase_template_int_int_bottomLeftCorner_int_int.cpp
new file mode 100644
index 000000000..a1edcc808
--- /dev/null
+++ b/doc/snippets/MatrixBase_template_int_int_bottomLeftCorner_int_int.cpp
@@ -0,0 +1,6 @@
+Matrix4i m = Matrix4i::Random();
+cout << "Here is the matrix m:" << endl << m << endl;
+cout << "Here is m.bottomLeftCorner<2,Dynamic>(2,2):" << endl;
+cout << m.bottomLeftCorner<2,Dynamic>(2,2) << endl;
+m.bottomLeftCorner<2,Dynamic>(2,2).setZero();
+cout << "Now the matrix m is:" << endl << m << endl;
diff --git a/doc/snippets/MatrixBase_template_int_int_bottomRightCorner_int_int.cpp b/doc/snippets/MatrixBase_template_int_int_bottomRightCorner_int_int.cpp
new file mode 100644
index 000000000..a65508fd8
--- /dev/null
+++ b/doc/snippets/MatrixBase_template_int_int_bottomRightCorner_int_int.cpp
@@ -0,0 +1,6 @@
+Matrix4i m = Matrix4i::Random();
+cout << "Here is the matrix m:" << endl << m << endl;
+cout << "Here is m.bottomRightCorner<2,Dynamic>(2,2):" << endl;
+cout << m.bottomRightCorner<2,Dynamic>(2,2) << endl;
+m.bottomRightCorner<2,Dynamic>(2,2).setZero();
+cout << "Now the matrix m is:" << endl << m << endl;
diff --git a/doc/snippets/MatrixBase_template_int_int_topLeftCorner_int_int.cpp b/doc/snippets/MatrixBase_template_int_int_topLeftCorner_int_int.cpp
new file mode 100644
index 000000000..fac761f63
--- /dev/null
+++ b/doc/snippets/MatrixBase_template_int_int_topLeftCorner_int_int.cpp
@@ -0,0 +1,6 @@
+Matrix4i m = Matrix4i::Random();
+cout << "Here is the matrix m:" << endl << m << endl;
+cout << "Here is m.topLeftCorner<2,Dynamic>(2,2):" << endl;
+cout << m.topLeftCorner<2,Dynamic>(2,2) << endl;
+m.topLeftCorner<2,Dynamic>(2,2).setZero();
+cout << "Now the matrix m is:" << endl << m << endl;
diff --git a/doc/snippets/MatrixBase_template_int_int_topRightCorner_int_int.cpp b/doc/snippets/MatrixBase_template_int_int_topRightCorner_int_int.cpp
new file mode 100644
index 000000000..a17acc004
--- /dev/null
+++ b/doc/snippets/MatrixBase_template_int_int_topRightCorner_int_int.cpp
@@ -0,0 +1,6 @@
+Matrix4i m = Matrix4i::Random();
+cout << "Here is the matrix m:" << endl << m << endl;
+cout << "Here is m.topRightCorner<2,Dynamic>(2,2):" << endl;
+cout << m.topRightCorner<2,Dynamic>(2,2) << endl;
+m.topRightCorner<2,Dynamic>(2,2).setZero();
+cout << "Now the matrix m is:" << endl << m << endl;
diff --git a/doc/snippets/RealQZ_compute.cpp b/doc/snippets/RealQZ_compute.cpp
new file mode 100644
index 000000000..a18da42e8
--- /dev/null
+++ b/doc/snippets/RealQZ_compute.cpp
@@ -0,0 +1,17 @@
+MatrixXf A = MatrixXf::Random(4,4);
+MatrixXf B = MatrixXf::Random(4,4);
+RealQZ<MatrixXf> qz(4); // preallocate space for 4x4 matrices
+qz.compute(A,B);  // A = Q S Z,  B = Q T Z
+
+// print original matrices and result of decomposition
+cout << "A:\n" << A << "\n" << "B:\n" << B << "\n";
+cout << "S:\n" << qz.matrixS() << "\n" << "T:\n" << qz.matrixT() << "\n";
+cout << "Q:\n" << qz.matrixQ() << "\n" << "Z:\n" << qz.matrixZ() << "\n";
+
+// verify precision
+cout << "\nErrors:"
+  << "\n|A-QSZ|: " << (A-qz.matrixQ()*qz.matrixS()*qz.matrixZ()).norm()
+  << ", |B-QTZ|: " << (B-qz.matrixQ()*qz.matrixT()*qz.matrixZ()).norm()
+  << "\n|QQ* - I|: " << (qz.matrixQ()*qz.matrixQ().adjoint() - MatrixXf::Identity(4,4)).norm()
+  << ", |ZZ* - I|: " << (qz.matrixZ()*qz.matrixZ().adjoint() - MatrixXf::Identity(4,4)).norm()
+  << "\n";
diff --git a/doc/special_examples/CMakeLists.txt b/doc/special_examples/CMakeLists.txt
index eeeae1d2a..0c9b3c3ba 100644
--- a/doc/special_examples/CMakeLists.txt
+++ b/doc/special_examples/CMakeLists.txt
@@ -10,11 +10,12 @@ endif(NOT EIGEN_TEST_NOQT)
 if(QT4_FOUND)
   add_executable(Tutorial_sparse_example Tutorial_sparse_example.cpp Tutorial_sparse_example_details.cpp)
   target_link_libraries(Tutorial_sparse_example ${EIGEN_STANDARD_LIBRARIES_TO_LINK_TO} ${QT_QTCORE_LIBRARY} ${QT_QTGUI_LIBRARY})
-
+  
   add_custom_command(
       TARGET Tutorial_sparse_example
       POST_BUILD
-      COMMAND Tutorial_sparse_example
-      ARGS ${CMAKE_CURRENT_BINARY_DIR}/../html/Tutorial_sparse_example.jpeg
+      COMMAND Tutorial_sparse_example ARGS ${CMAKE_CURRENT_BINARY_DIR}/../html/Tutorial_sparse_example.jpeg
   )
+                     
+  add_dependencies(all_examples Tutorial_sparse_example)
 endif(QT4_FOUND)
diff --git a/doc/special_examples/Tutorial_sparse_example_details.cpp b/doc/special_examples/Tutorial_sparse_example_details.cpp
index 8c3020b63..7d820b44a 100644
--- a/doc/special_examples/Tutorial_sparse_example_details.cpp
+++ b/doc/special_examples/Tutorial_sparse_example_details.cpp
@@ -11,8 +11,8 @@ void insertCoefficient(int id, int i, int j, double w, std::vector<T>& coeffs,
   int n = boundary.size();
   int id1 = i+j*n;
 
-        if(i==-1 || i==n) b(id) -= w * boundary(j); // constrained coeffcieint
-  else  if(j==-1 || j==n) b(id) -= w * boundary(i); // constrained coeffcieint
+        if(i==-1 || i==n) b(id) -= w * boundary(j); // constrained coefficient
+  else  if(j==-1 || j==n) b(id) -= w * boundary(i); // constrained coefficient
   else  coeffs.push_back(T(id,id1,w));              // unknown coefficient
 }