diff --git a/doc/deal.ico b/doc/deal.ico
index 88ddb74ee6fe..b7cfd41ab3af 100644
Binary files a/doc/deal.ico and b/doc/deal.ico differ
diff --git a/doc/doxygen/CMakeLists.txt b/doc/doxygen/CMakeLists.txt
index d13960cf461a..41a1cc20102d 100644
--- a/doc/doxygen/CMakeLists.txt
+++ b/doc/doxygen/CMakeLists.txt
@@ -90,32 +90,42 @@ ADD_CUSTOM_COMMAND(
 # Finalize the doxygen configuration:
 #
 file(GLOB _doxygen_input
+  ${CMAKE_CURRENT_BINARY_DIR}/tutorial/*.h
+  )
+LIST(APPEND _doxygen_input
+  ${CMAKE_SOURCE_DIR}/include/
+  ${CMAKE_BINARY_DIR}/include/
+  ${CMAKE_CURRENT_SOURCE_DIR}/headers/
+  ${CMAKE_SOURCE_DIR}/doc/news/
+  ${CMAKE_CURRENT_BINARY_DIR}/tutorial/tutorial.h
+  ${CMAKE_SOURCE_DIR}/contrib/parameter_gui/
+  )
+TO_STRING(_doxygen_input_string ${_doxygen_input})
+
+SET(_doxygen_image_path
+  ${CMAKE_CURRENT_SOURCE_DIR}/images
+  ${CMAKE_SOURCE_DIR}/contrib/parameter_gui/images
+  ${CMAKE_CURRENT_BINARY_DIR}/images
+  )
+TO_STRING(_doxygen_image_path_string ${_doxygen_image_path})
+
+file(GLOB _doxygen_depend
   ${CMAKE_CURRENT_SOURCE_DIR}/headers/*.h
   ${CMAKE_SOURCE_DIR}/contrib/parameter_gui/*.h
   ${CMAKE_SOURCE_DIR}/contrib/parameter_gui/main.cpp
   ${CMAKE_SOURCE_DIR}/doc/news/*.h
   ${CMAKE_SOURCE_DIR}/include/deal.II/**/*.h
   )
-LIST(APPEND _doxygen_input
+LIST(APPEND _doxygen_depend
   ${CMAKE_BINARY_DIR}/include/deal.II/base/config.h
   ${CMAKE_CURRENT_BINARY_DIR}/tutorial/tutorial.h
   )
 FOREACH(_step ${DEAL_II_STEPS})
   GET_FILENAME_COMPONENT(_step "${_step}" NAME)
-  LIST(APPEND _doxygen_input
+  LIST(APPEND _doxygen_depend
     ${CMAKE_CURRENT_BINARY_DIR}/tutorial/${_step}.h
     )
 ENDFOREACH()
-TO_STRING(_doxygen_input_string ${_doxygen_input})
-
-file(GLOB _doxygen_image_path
-  ${CMAKE_CURRENT_SOURCE_DIR}/images
-  ${CMAKE_SOURCE_DIR}/examples/*/doc
-  ${CMAKE_SOURCE_DIR}/contrib/parameter_gui/images
-
-  ${CMAKE_CURRENT_BINARY_DIR}/images
-  )
-TO_STRING(_doxygen_image_path_string ${_doxygen_image_path})
 
 FILE(APPEND "${CMAKE_CURRENT_BINARY_DIR}/options.dox"
   "
@@ -139,7 +149,7 @@ ADD_CUSTOM_COMMAND(
     ${CMAKE_CURRENT_BINARY_DIR}/options.dox
     ${CMAKE_CURRENT_BINARY_DIR}/header.html
     ${CMAKE_CURRENT_BINARY_DIR}/footer.html
-    ${_doxygen_input}
+    ${_doxygen_depend}
   COMMENT "Generating documentation via doxygen."
   VERBATIM
   )
diff --git a/doc/doxygen/options.dox.in b/doc/doxygen/options.dox.in
index 00a5dad15fa7..14824a0ee2c9 100644
--- a/doc/doxygen/options.dox.in
+++ b/doc/doxygen/options.dox.in
@@ -25,7 +25,9 @@ CASE_SENSE_NAMES       = YES
 
 
 INLINE_INHERITED_MEMB  = NO
-STRIP_FROM_PATH        = @CMAKE_SOURCE_DIR@ @CMAKE_BINARY_DIR@
+STRIP_FROM_PATH        = @CMAKE_SOURCE_DIR@/include @CMAKE_BINARY_DIR@/include
+STRIP_FROM_INC_PATH    = @CMAKE_SOURCE_DIR@/include @CMAKE_BINARY_DIR@/include
+FULL_PATH_NAMES        = YES
 JAVADOC_AUTOBRIEF      = NO
 INHERIT_DOCS           = YES
 TAB_SIZE               = 8
@@ -56,7 +58,7 @@ SHOW_USED_FILES        = YES
 
 QUIET                  = YES
 WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = YES
+WARN_IF_UNDOCUMENTED   = NO
 WARN_IF_DOC_ERROR      = YES
 
 #---------------------------------------------------------------------------
@@ -64,6 +66,7 @@ WARN_IF_DOC_ERROR      = YES
 #---------------------------------------------------------------------------
 
 INPUT                  =
+RECURSIVE              = YES
 EXCLUDE_PATTERNS       = *.templates.h
 EXAMPLE_PATH           = @CMAKE_BINARY_DIR@/doc/doxygen/tutorial \
                          @CMAKE_SOURCE_DIR@/examples/doxygen
diff --git a/doc/news/changes.h b/doc/news/changes.h
index f53f3a2dde80..8fb0733749fa 100644
--- a/doc/news/changes.h
+++ b/doc/news/changes.h
@@ -79,8 +79,8 @@ inconvenience this causes.
   inheritance is gone. For the most part, this should not lead to any
   incompatibilities except in cases where you accessed members of
   DataOutBase through their derived classes. For example, it was possible
-  to write <code>DataOut@<2@>::Patch@<2,2@></code> even though the
-  <code>Patch</code> class is actually declared in DataOutBase. Since
+  to write DataOut::Patch even though the
+  Patch class is actually declared in DataOutBase. Since
   the inheritance is now gone, this is no longer possible and one
   actually has to write DataOutBase::Patch instead. Using this form
   turns out to be compatible also with older versions of deal.II.
diff --git a/include/deal.II/algorithms/theta_timestepping.h b/include/deal.II/algorithms/theta_timestepping.h
index b8a90611ecd6..f6a30bc600d5 100644
--- a/include/deal.II/algorithms/theta_timestepping.h
+++ b/include/deal.II/algorithms/theta_timestepping.h
@@ -180,7 +180,7 @@ namespace Algorithms
    * for us). Here, we first get the time step size from the AnyData
    * object that was provided as input. Then, if we are in the first
    * step or if the timestep has changed, we fill the local matrix
-   * <tt>m</tt>, such that with the given matrix \f$M\f$, it becomes
+   * $m$, such that with the given matrix $M$, it becomes
    * \f[
    * m = I - \Delta t M.
    * \f]
@@ -219,11 +219,11 @@ namespace Algorithms
     /**
      * The timestepping scheme.
      *
-     * @param `in` is ignored by
+     * @param in is ignored by
      * ThetaTimestepping, but is merged into the AnyData objects used
      * as input for the operators #op_explicit and #op_implicit.
      *
-     * @param `out` in its first argument must contain a pointer to a
+     * @param out in its first argument must contain a pointer to a
      * `VECTOR`, which contains the initial value when the operator is
      * called. It contains the final value when the operator returns.
      */
@@ -334,10 +334,10 @@ namespace Algorithms
      * with name "Current time solution". It should obtain the current
      * time and time step size from explicit_data().
      *
-     * Its return value is <i>Mu+cF(u)</i>, where <i>u</i> is the
-     * current state vector, <i>M</i> the mass matrix, <i>F</i> the
-     * operator in space and <i>c</i> is the adjusted
-     * time step size \f$ (1-\theta) \Delta t\f$.
+     * Its return value is $ Mu+cF(u) $, where $u$ is the
+     * current state vector, $M$ the mass matrix, $F$ the
+     * operator in space and $c$ is the adjusted
+     * time step size $(1-\theta) \Delta t$.
      */
     SmartPointer<Operator<VECTOR>, ThetaTimestepping<VECTOR> > op_explicit;
 
diff --git a/include/deal.II/fe/fe_tools.h b/include/deal.II/fe/fe_tools.h
index 854f26041f06..3938862055fd 100644
--- a/include/deal.II/fe/fe_tools.h
+++ b/include/deal.II/fe/fe_tools.h
@@ -707,15 +707,15 @@ namespace FETools
    * other:
    *
    * - It interpolates directly from every cell of @p dof1 to the
-   *   corresponding cell of @dof2 using the interpolation matrix of the
+   *   corresponding cell of `dof2` using the interpolation matrix of the
    *   finite element spaces used on these cells and provided by
    *   the finite element objects involved. This step is done using the
    *   FETools::interpolate() function.
-   * - It then performs a loop over all non-active cells of @dof2. If
+   * - It then performs a loop over all non-active cells of `dof2`. If
    *   such a non-active cell has at least one active child, then we
    *   call the children of this cell a "patch". We then interpolate
    *   from the children of this patch to the patch, using the finite
-   *   element space associated with @p dof2 and immediately interpolate
+   *   element space associated with `dof2` and immediately interpolate
    *   back to the children. In essence, this information throws away
    *   all information in the solution vector that lives on a scale
    *   smaller than the patch cell.
diff --git a/include/deal.II/grid/filtered_iterator.h b/include/deal.II/grid/filtered_iterator.h
index 6356cd160a4d..5916dd4d1e55 100644
--- a/include/deal.II/grid/filtered_iterator.h
+++ b/include/deal.II/grid/filtered_iterator.h
@@ -357,7 +357,7 @@ namespace IteratorFilters
  * @endcode
  * Note that by the @p set_to_next_positive call the first cell with
  * a set user flag was assigned to the @p begin iterator. For the
- * #end iterator, no such call was necessary, since the past-the-end
+ * end iterator, no such call was necessary, since the past-the-end
  * iterator always satisfies all predicates.
  *
  * The same can be achieved by the following snippet, though harder to read:
diff --git a/include/deal.II/grid/grid_generator.h b/include/deal.II/grid/grid_generator.h
index 6918354afdf8..44a45c0edf66 100644
--- a/include/deal.II/grid/grid_generator.h
+++ b/include/deal.II/grid/grid_generator.h
@@ -57,7 +57,7 @@ namespace GridGenerator
    * Initialize the given triangulation with a hypercube (line in 1D,
    * square in 2D, etc) consisting of exactly one cell. The hypercube
    * volume is the tensor product interval
-   * \f$ [left,right]^{\text{dim}}\f$ in the present number of
+   * $[left,right]^{\text{dim}}$ in the present number of
    * dimensions, where the limits are given as arguments. They default
    * to zero and unity, then producing the unit hypercube. If the
    * argument `colorize` is false, all boundary indicators are set to
diff --git a/include/deal.II/grid/tria_iterator.h b/include/deal.II/grid/tria_iterator.h
index 013cb00bcc1b..51513ba14ba5 100644
--- a/include/deal.II/grid/tria_iterator.h
+++ b/include/deal.II/grid/tria_iterator.h
@@ -464,7 +464,7 @@ class TriaRawIterator : public std::iterator<std::bidirectional_iterator_tag,Acc
    * <li> The index of a cell inside the level.</li>
    * </ol>
    *
-   * @Note: the ordering is not consistent between different processor in
+   * @note The ordering is not consistent between different processor in
    * a parallel::distributed::Triangulation because we rely on index(),
    * which is likely not the same.
    */
diff --git a/include/deal.II/lac/trilinos_vector_base.h b/include/deal.II/lac/trilinos_vector_base.h
index 9d5a7e3cfc5f..2289b3304d4f 100644
--- a/include/deal.II/lac/trilinos_vector_base.h
+++ b/include/deal.II/lac/trilinos_vector_base.h
@@ -794,7 +794,7 @@ namespace TrilinosWrappers
 
     /**
      *  Output of vector in user-defined format in analogy to the
-     *  dealii::Vector<number> class.
+     *  dealii::Vector class.
      */
     void print (const char *format = 0) const;
 
diff --git a/include/deal.II/meshworker/loop.h b/include/deal.II/meshworker/loop.h
index 911f0435c9ec..391eb166d02b 100644
--- a/include/deal.II/meshworker/loop.h
+++ b/include/deal.II/meshworker/loop.h
@@ -156,10 +156,6 @@ namespace MeshWorker
    * @param cell_worker defines the local action on each cell.
    * @param boundary_worker defines the local action on boundary faces
    * @param face_worker defines the local action on interior faces.
-   * @param cells_first determines, whether, on a given cell, face or cell
-   *        integrals are to be  dealt with first. Note that independent of the
-   *        value of this flag, cell and face integrals of a given cell are
-   *        all taken care of before moving to the next cell.
    * @param loop_control control structure to specify what actions should be performed.
    *
    * @ingroup MeshWorker
diff --git a/include/deal.II/numerics/data_out.h b/include/deal.II/numerics/data_out.h
index 0bc554148ceb..adba6b9e95f1 100644
--- a/include/deal.II/numerics/data_out.h
+++ b/include/deal.II/numerics/data_out.h
@@ -148,7 +148,7 @@ namespace internal
  * this pair of functions and they return a non-active cell, then an exception
  * will be thrown.
  *
- * @precondition This class only makes sense if the first template
+ * @pre This class only makes sense if the first template
  * argument, <code>dim</code> equals the dimension of the
  * DoFHandler type given as the second template argument, i.e., if
  * <code>dim == DH::dimension</code>. This redundancy is a historical
diff --git a/include/deal.II/numerics/data_out_faces.h b/include/deal.II/numerics/data_out_faces.h
index 1a6f9427e2c9..7eaaf7b109f4 100644
--- a/include/deal.II/numerics/data_out_faces.h
+++ b/include/deal.II/numerics/data_out_faces.h
@@ -108,7 +108,7 @@ namespace internal
  * applications certainly exist, for which the author is not
  * imaginative enough.
  *
- * @precondition This class only makes sense if the first template
+ * @pre This class only makes sense if the first template
  * argument, <code>dim</code> equals the dimension of the
  * DoFHandler type given as the second template argument, i.e., if
  * <code>dim == DH::dimension</code>. This redundancy is a historical
diff --git a/include/deal.II/numerics/data_out_rotation.h b/include/deal.II/numerics/data_out_rotation.h
index 1f6ea01a9466..0099d6d8778f 100644
--- a/include/deal.II/numerics/data_out_rotation.h
+++ b/include/deal.II/numerics/data_out_rotation.h
@@ -114,7 +114,7 @@ namespace internal
  * It is in the responsibility of the user to make sure that the
  * radial variable attains only non-negative values.
  *
- * @precondition This class only makes sense if the first template
+ * @pre This class only makes sense if the first template
  * argument, <code>dim</code> equals the dimension of the
  * DoFHandler type given as the second template argument, i.e., if
  * <code>dim == DH::dimension</code>. This redundancy is a historical