Doxygen documentation improvement

4 files changed, 174 insertions, 175 deletions

diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h
index 474f8699..b557727b 100644
--- a/src/common/doc/examples.h
+++ b/src/common/doc/examples.h
@@ -1,96 +1,98 @@
 // List of GUDHI examples - Doxygen needs at least a file tag to analyse comments
 // In user_version, `find . -name "*.cpp"` in example and utilities folders
 /*! @file Examples
- * @example Alpha_complex/Alpha_complex_from_off.cpp
- * @example Alpha_complex/Alpha_complex_from_points.cpp
- * @example Bottleneck_distance/bottleneck_basic_example.cpp
- * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
- * @example Witness_complex/example_nearest_landmark_table.cpp
- * @example Witness_complex/example_witness_complex_off.cpp
- * @example Witness_complex/example_witness_complex_sphere.cpp
- * @example Witness_complex/example_strong_witness_complex_off.cpp
- * @example Simplex_tree/mini_simplex_tree.cpp
- * @example Simplex_tree/graph_expansion_with_blocker.cpp
- * @example Simplex_tree/simple_simplex_tree.cpp
- * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp
- * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp
- * @example Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp
- * @example Persistent_cohomology/plain_homology.cpp
- * @example Persistent_cohomology/persistence_from_file.cpp
- * @example Persistent_cohomology/rips_persistence_step_by_step.cpp
- * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp
- * @example Persistent_cohomology/custom_persistence_sort.cpp
- * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp
- * @example Persistent_cohomology/rips_multifield_persistence.cpp
- * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
- * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
- * @example Skeleton_blocker/Skeleton_blocker_link.cpp
- * @example Contraction/Garland_heckbert.cpp
- * @example Contraction/Rips_contraction.cpp
- * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
- * @example common/example_CGAL_3D_points_off_reader.cpp
- * @example common/example_vector_double_points_off_reader.cpp
- * @example common/example_CGAL_points_off_reader.cpp
- * @example Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp
- * @example Rips_complex/example_one_skeleton_rips_from_points.cpp
- * @example Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp
- * @example Rips_complex/example_rips_complex_from_off_file.cpp
- * @example Persistence_representations/persistence_intervals.cpp
- * @example Persistence_representations/persistence_vectors.cpp
- * @example Persistence_representations/persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_landscape_on_grid.cpp
- * @example Persistence_representations/persistence_landscape.cpp
- * @example Tangential_complex/example_basic.cpp
- * @example Tangential_complex/example_with_perturb.cpp
- * @example Subsampling/example_custom_distance.cpp
- * @example Subsampling/example_choose_n_farthest_points.cpp
- * @example Subsampling/example_sparsify_point_set.cpp
- * @example Subsampling/example_pick_n_random_points.cpp
- * @example Nerve_GIC/CoordGIC.cpp
- * @example Nerve_GIC/Nerve.cpp
- * @example Nerve_GIC/FuncGIC.cpp
- * @example Nerve_GIC/VoronoiGIC.cpp
- * @example Spatial_searching/example_spatial_searching.cpp
- * @example Alpha_complex/alpha_complex_3d_persistence.cpp
- * @example Alpha_complex/alpha_complex_persistence.cpp
- * @example Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp
- * @example Bottleneck_distance/bottleneck_distance.cpp
- * @example Witness_complex/weak_witness_persistence.cpp
- * @example Witness_complex/strong_witness_persistence.cpp
- * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp
- * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp
- * @example common/off_file_from_shape_generator.cpp
- * @example Rips_complex/rips_distance_matrix_persistence.cpp
- * @example Rips_complex/rips_persistence.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
- * @example Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
- * @example Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp
- * @example Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp
- * @example Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp
- * @example Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp
- * @example Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp
- * @example Persistence_representations/persistence_heat_maps/create_pssk.cpp
- * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
- * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
- * @example Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
- * @example Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp
- * @example Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp
- * @example Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp
- * @example Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp
- * @example Persistence_representations/persistence_vectors/average_persistence_vectors.cpp
- * @example Persistence_representations/persistence_vectors/create_persistence_vectors.cpp
- * @example Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
- * @example Persistence_representations/persistence_landscapes/average_landscapes.cpp
- * @example Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp
- * @example Persistence_representations/persistence_landscapes/create_landscapes.cpp
- * @example Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp
- * @example Persistence_representations/persistence_landscapes/plot_landscapes.cpp
+ * \section Alpha_complex_examples Alpha complex
+ * @example Alpha_complex_from_off.cpp
+ * @example Alpha_complex_from_points.cpp
+ * \section bottleneck_examples bottleneck
+ * @example bottleneck_basic_example.cpp
+ * @example alpha_rips_persistence_bottleneck_distance.cpp
+ * @example example_nearest_landmark_table.cpp
+ * @example example_witness_complex_off.cpp
+ * @example example_witness_complex_sphere.cpp
+ * @example example_strong_witness_complex_off.cpp
+ * @example mini_simplex_tree.cpp
+ * @example graph_expansion_with_blocker.cpp
+ * @example simple_simplex_tree.cpp
+ * @example simplex_tree_from_cliques_of_graph.cpp
+ * @example example_alpha_shapes_3_simplex_tree_from_off_file.cpp
+ * @example cech_complex_cgal_mini_sphere_3d.cpp
+ * @example plain_homology.cpp
+ * @example persistence_from_file.cpp
+ * @example rips_persistence_step_by_step.cpp
+ * @example rips_persistence_via_boundary_matrix.cpp
+ * @example custom_persistence_sort.cpp
+ * @example persistence_from_simple_simplex_tree.cpp
+ * @example rips_multifield_persistence.cpp
+ * @example Skeleton_blocker_from_simplices.cpp
+ * @example Skeleton_blocker_iteration.cpp
+ * @example Skeleton_blocker_link.cpp
+ * @example Garland_heckbert.cpp
+ * @example Rips_contraction.cpp
+ * @example Random_bitmap_cubical_complex.cpp
+ * @example example_CGAL_3D_points_off_reader.cpp
+ * @example example_vector_double_points_off_reader.cpp
+ * @example example_CGAL_points_off_reader.cpp
+ * @example example_one_skeleton_rips_from_distance_matrix.cpp
+ * @example example_one_skeleton_rips_from_points.cpp
+ * @example example_rips_complex_from_csv_distance_matrix_file.cpp
+ * @example example_rips_complex_from_off_file.cpp
+ * @example persistence_intervals.cpp
+ * @example persistence_vectors.cpp
+ * @example persistence_heat_maps.cpp
+ * @example persistence_landscape_on_grid.cpp
+ * @example persistence_landscape.cpp
+ * @example example_basic.cpp
+ * @example example_with_perturb.cpp
+ * @example example_custom_distance.cpp
+ * @example example_choose_n_farthest_points.cpp
+ * @example example_sparsify_point_set.cpp
+ * @example example_pick_n_random_points.cpp
+ * @example CoordGIC.cpp
+ * @example Nerve.cpp
+ * @example FuncGIC.cpp
+ * @example VoronoiGIC.cpp
+ * @example example_spatial_searching.cpp
+ * @example alpha_complex_3d_persistence.cpp
+ * @example alpha_complex_persistence.cpp
+ * @example Weighted_alpha_complex_3d_from_points.cpp
+ * @example bottleneck_distance.cpp
+ * @example weak_witness_persistence.cpp
+ * @example strong_witness_persistence.cpp
+ * @example cubical_complex_persistence.cpp
+ * @example periodic_cubical_complex_persistence.cpp
+ * @example off_file_from_shape_generator.cpp
+ * @example rips_distance_matrix_persistence.cpp
+ * @example rips_persistence.cpp
+ * @example persistence_landscapes_on_grid/create_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp
+ * @example persistence_landscapes_on_grid/average_landscapes_on_grid.cpp
+ * @example persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp
+ * @example persistence_intervals/compute_number_of_dominant_intervals.cpp
+ * @example persistence_intervals/plot_persistence_Betti_numbers.cpp
+ * @example persistence_intervals/plot_persistence_intervals.cpp
+ * @example persistence_intervals/plot_histogram_of_intervals_lengths.cpp
+ * @example persistence_intervals/compute_bottleneck_distance.cpp
+ * @example persistence_heat_maps/create_pssk.cpp
+ * @example persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp
+ * @example persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp
+ * @example persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp
+ * @example persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp
+ * @example persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp
+ * @example persistence_heat_maps/average_persistence_heat_maps.cpp
+ * @example persistence_heat_maps/plot_persistence_heat_map.cpp
+ * @example persistence_heat_maps/create_persistence_heat_maps.cpp
+ * @example persistence_vectors/plot_persistence_vectors.cpp
+ * @example persistence_vectors/compute_distance_of_persistence_vectors.cpp
+ * @example persistence_vectors/average_persistence_vectors.cpp
+ * @example persistence_vectors/create_persistence_vectors.cpp
+ * @example persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp
+ * @example persistence_landscapes/average_landscapes.cpp
+ * @example persistence_landscapes/compute_scalar_product_of_landscapes.cpp
+ * @example persistence_landscapes/create_landscapes.cpp
+ * @example persistence_landscapes/compute_distance_of_landscapes.cpp
+ * @example persistence_landscapes/plot_landscapes.cpp
  */
  
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index c2e63a24..313184b6 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -40,11 +40,8 @@ make \endverbatim
  * \subsection documentationgeneration Documentation
  * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required.
  * Run the following command in a terminal:
-\verbatim
-make doxygen
-# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/
-# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder`
-\endverbatim
+ * \verbatim make doxygen \endverbatim
+ * Documentation will be generated in a folder named <code>html</code>.
  *
  * \subsection helloworld Hello world !
  * The <a target="_blank" href="https://github.com/GUDHI/hello-gudhi-world">Hello world for GUDHI</a>
@@ -57,7 +54,7 @@ make doxygen
  * 
  * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
  * Library</a> (GMP) and will not be built if GMP is not installed:
- * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * \li <a href="rips_multifield_persistence_8cpp-example.html">
  * Persistent_cohomology/rips_multifield_persistence.cpp</a>
  *
  * Having GMP version 4.2 or higher installed is recommended.
@@ -75,55 +72,55 @@ make doxygen
  * 
  * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
  * Library</a> (CGAL \cite cgal:eb-19b) and will not be built if CGAL version 4.11.0 or higher is not installed:
- * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
+ * \li <a href="example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
  * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
- * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
+ * \li <a href="strong_witness_persistence_8cpp-example.html">
  * Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
+ * \li <a href="weak_witness_persistence_8cpp-example.html">
  * Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html">
+ * \li <a href="example_strong_witness_complex_off_8cpp-example.html">
  * Witness_complex/example_strong_witness_complex_off.cpp</a>
- * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html">
+ * \li <a href="example_witness_complex_off_8cpp-example.html">
  * Witness_complex/example_witness_complex_off.cpp</a>
- * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html">
+ * \li <a href="example_witness_complex_sphere_8cpp-example.html">
  * Witness_complex/example_witness_complex_sphere.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * \li <a href="alpha_complex_from_off_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * \li <a href="alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * \li <a href="custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * \li <a href="alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
  * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
- * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html">
+ * \li <a href="bottleneck_basic_example_8cpp-example.html">
  * Bottleneck_distance/bottleneck_basic_example.cpp</a>
- * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html">
+ * \li <a href="bottleneck_read_file_8cpp-example.html">
  * Bottleneck_distance/bottleneck_distance.cpp</a>
- * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html">
+ * \li <a href="coord_g_i_c_8cpp-example.html">
  * Nerve_GIC/CoordGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html">
+ * \li <a href="func_g_i_c_8cpp-example.html">
  * Nerve_GIC/FuncGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html">
+ * \li <a href="nerve_8cpp-example.html">
  * Nerve_GIC/Nerve.cpp</a>
- * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html">
+ * \li <a href="voronoi_g_i_c_8cpp-example.html">
  * Nerve_GIC/VoronoiGIC.cpp</a>
- * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * \li <a href="example_spatial_searching_8cpp-example.html">
  * Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * \li <a href="example_choose_n_farthest_points_8cpp-example.html">
  * Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * \li <a href="example_pick_n_random_points_8cpp-example.html">
  * Subsampling/example_pick_n_random_points.cpp</a>
- * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
+ * \li <a href="example_sparsify_point_set_8cpp-example.html">
  * Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * \li <a href="example_basic_8cpp-example.html">
  * Tangential_complex/example_basic.cpp</a>
- * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * \li <a href="example_with_perturb_8cpp-example.html">
  * Tangential_complex/example_with_perturb.cpp</a>
- * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
+ * \li <a href="weighted_alpha_complex_3d_from_points_8cpp-example.html">
  * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
  *
  * \subsection eigen Eigen
@@ -133,41 +130,41 @@ make doxygen
  * 
  * The following examples/utilities require the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen</a> and will not be
  * built if Eigen is not installed:
- * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * \li <a href="alpha_complex_from_off_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * \li <a href="alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
+ * \li <a href="weighted_alpha_complex_3d_from_points_8cpp-example.html">
  * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
- * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * \li <a href="alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
  * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * \li <a href="custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * \li <a href="example_spatial_searching_8cpp-example.html">
  * Spatial_searching/example_spatial_searching.cpp</a>
- * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * \li <a href="example_choose_n_farthest_points_8cpp-example.html">
  * Subsampling/example_choose_n_farthest_points.cpp</a>
- * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * \li <a href="example_pick_n_random_points_8cpp-example.html">
  * Subsampling/example_pick_n_random_points.cpp</a>
- * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
+ * \li <a href="example_sparsify_point_set_8cpp-example.html">
  * Subsampling/example_sparsify_point_set.cpp</a>
- * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * \li <a href="example_basic_8cpp-example.html">
  * Tangential_complex/example_basic.cpp</a>
- * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * \li <a href="example_with_perturb_8cpp-example.html">
  * Tangential_complex/example_with_perturb.cpp</a>
- * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
+ * \li <a href="strong_witness_persistence_8cpp-example.html">
  * Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
+ * \li <a href="weak_witness_persistence_8cpp-example.html">
  * Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html">
+ * \li <a href="example_strong_witness_complex_off_8cpp-example.html">
  * Witness_complex/example_strong_witness_complex_off.cpp</a>
- * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html">
+ * \li <a href="example_witness_complex_off_8cpp-example.html">
  * Witness_complex/example_witness_complex_off.cpp</a>
- * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html">
+ * \li <a href="example_witness_complex_sphere_8cpp-example.html">
  * Witness_complex/example_witness_complex_sphere.cpp</a>
  *
  * \subsection tbb Threading Building Blocks
@@ -178,67 +175,67 @@ make doxygen
  * Having Intel&reg; TBB installed is recommended to parallelize and accelerate some GUDHI computations.
  * 
  * The following examples/utilities are using Intel&reg; TBB if installed:
- * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * \li <a href="alpha_complex_from_off_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
- * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * \li <a href="alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
+ * \li <a href="bitmap_cubical_complex_8cpp-example.html">
  * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a>
- * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
+ * \li <a href="bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
  * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a>
- * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html">
+ * \li <a href="random_bitmap_cubical_complex_8cpp-example.html">
  * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a>
- * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html">
+ * \li <a href="coord_g_i_c_8cpp-example.html">
  * Nerve_GIC/CoordGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html">
+ * \li <a href="func_g_i_c_8cpp-example.html">
  * Nerve_GIC/FuncGIC.cpp</a>
- * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html">
+ * \li <a href="nerve_8cpp-example.html">
  * Nerve_GIC/Nerve.cpp</a>
- * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html">
+ * \li <a href="voronoi_g_i_c_8cpp-example.html">
  * Nerve_GIC/VoronoiGIC.cpp</a>
- * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
+ * \li <a href="simple_simplex_tree_8cpp-example.html">
  * Simplex_tree/simple_simplex_tree.cpp</a>
- * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
+ * \li <a href="example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
  * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
- * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html">
+ * \li <a href="simplex_tree_from_cliques_of_graph_8cpp-example.html">
  * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a>
- * \li <a href="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html">
+ * \li <a href="graph_expansion_with_blocker_8cpp-example.html">
  * Simplex_tree/graph_expansion_with_blocker.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * \li <a href="alpha_complex_persistence_8cpp-example.html">
  * Persistent_cohomology/alpha_complex_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html">
+ * \li <a href="rips_persistence_via_boundary_matrix_8cpp-example.html">
  * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a>
- * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html">
+ * \li <a href="persistence_from_file_8cpp-example.html">
  * Persistent_cohomology/persistence_from_file.cpp</a>
- * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html">
+ * \li <a href="persistence_from_simple_simplex_tree_8cpp-example.html">
  * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a>
- * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html">
+ * \li <a href="plain_homology_8cpp-example.html">
  * Persistent_cohomology/plain_homology.cpp</a>
- * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html">
+ * \li <a href="rips_multifield_persistence_8cpp-example.html">
  * Persistent_cohomology/rips_multifield_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html">
+ * \li <a href="rips_persistence_step_by_step_8cpp-example.html">
  * Persistent_cohomology/rips_persistence_step_by_step.cpp</a>
- * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
+ * \li <a href="custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html">
+ * \li <a href="example_one_skeleton_rips_from_points_8cpp-example.html">
  * Rips_complex/example_one_skeleton_rips_from_points.cpp</a>
- * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html">
+ * \li <a href="example_rips_complex_from_off_file_8cpp-example.html">
  * Rips_complex/example_rips_complex_from_off_file.cpp</a>
- * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html">
+ * \li <a href="rips_distance_matrix_persistence_8cpp-example.html">
  * Rips_complex/rips_distance_matrix_persistence.cpp</a>
- * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html">
+ * \li <a href="rips_persistence_8cpp-example.html">
  * Rips_complex/rips_persistence.cpp</a>
- * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
+ * \li <a href="strong_witness_persistence_8cpp-example.html">
  * Witness_complex/strong_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html">
+ * \li <a href="weak_witness_persistence_8cpp-example.html">
  * Witness_complex/weak_witness_persistence.cpp</a>
- * \li <a href="_witness_complex_2example_nearest_landmark_table_8cpp-example.html">
+ * \li <a href="example_nearest_landmark_table_8cpp-example.html">
  * Witness_complex/example_nearest_landmark_table.cpp</a>
  *
  * \section Contributions Bug reports and contributions
diff --git a/src/common/include/gudhi/Points_3D_off_io.h b/src/common/include/gudhi/Points_3D_off_io.h
index 39b79c96..4f74fd4b 100644
--- a/src/common/include/gudhi/Points_3D_off_io.h
+++ b/src/common/include/gudhi/Points_3D_off_io.h
@@ -125,7 +125,7 @@ class Points_3D_off_visitor_reader {
  * This example loads points from an OFF file and builds a vector of CGAL points in dimension 3.
  * Then, it is asked to display the points.
  * 
- * @include common/example_CGAL_3D_points_off_reader.cpp
+ * @include example_CGAL_3D_points_off_reader.cpp
  * 
  * When launching:
  * 
@@ -134,7 +134,7 @@ class Points_3D_off_visitor_reader {
  *
  * the program output is:
  * 
- * @include common/cgal3Doffreader_result.txt
+ * @include cgal3Doffreader_result.txt
  */
 template<typename Point_3>
 class Points_3D_off_reader {
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
index 9dc40568..3aa8afd8 100644
--- a/src/common/include/gudhi/Points_off_io.h
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -107,7 +107,7 @@ class Points_off_visitor_reader {
  * This example loads points from an OFF file and builds a vector of points (vector of double).
  * Then, it is asked to display the points.
  * 
- * \include common/example_vector_double_points_off_reader.cpp
+ * \include example_vector_double_points_off_reader.cpp
  * 
  * When launching:
  * 
@@ -116,7 +116,7 @@ class Points_off_visitor_reader {
  *
  * the program outputs a file ../../data/points/alphacomplexdoc.off.txt:
  * 
- * \include common/vectordoubleoffreader_result.txt
+ * \include vectordoubleoffreader_result.txt
  */
 template<typename Point_d>
 class Points_off_reader {