diff --git a/AABB_tree/doc/AABB_tree/Doxyfile.in b/AABB_tree/doc/AABB_tree/Doxyfile.in
index 44af18375c1..5255b5ada37 100644
--- a/AABB_tree/doc/AABB_tree/Doxyfile.in
+++ b/AABB_tree/doc/AABB_tree/Doxyfile.in
@@ -2,9 +2,6 @@
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - 3D Fast Intersection and Distance Computation (AABB Tree)"
 
-INPUT                      =  ${CMAKE_SOURCE_DIR}/AABB_tree/doc/AABB_tree/ \ 
-                              ${CMAKE_SOURCE_DIR}/AABB_tree/include
-
 EXTRACT_ALL                =  false
 HIDE_UNDOC_MEMBERS         =  true
 HIDE_UNDOC_CLASSES         =  true
diff --git a/Advancing_front_surface_reconstruction/doc/Advancing_front_surface_reconstruction/Doxyfile.in b/Advancing_front_surface_reconstruction/doc/Advancing_front_surface_reconstruction/Doxyfile.in
index cb6bc2d0850..ca7edf148ad 100644
--- a/Advancing_front_surface_reconstruction/doc/Advancing_front_surface_reconstruction/Doxyfile.in
+++ b/Advancing_front_surface_reconstruction/doc/Advancing_front_surface_reconstruction/Doxyfile.in
@@ -1,10 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Advancing Front Surface Reconstruction"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Advancing_front_surface_reconstruction/doc/Advancing_front_surface_reconstruction/ \
-                              ${CMAKE_SOURCE_DIR}/Advancing_front_surface_reconstruction/include
-
 EXTRACT_ALL                =  false
 HIDE_UNDOC_MEMBERS         =  true
 HIDE_UNDOC_CLASSES         =  true
diff --git a/Barycentric_coordinates_2/doc/Barycentric_coordinates_2/Doxyfile.in b/Barycentric_coordinates_2/doc/Barycentric_coordinates_2/Doxyfile.in
index c07670399ef..1378213fbe2 100644
--- a/Barycentric_coordinates_2/doc/Barycentric_coordinates_2/Doxyfile.in
+++ b/Barycentric_coordinates_2/doc/Barycentric_coordinates_2/Doxyfile.in
@@ -1,10 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME               =  "CGAL ${CGAL_CREATED_VERSION_NUM} - 2D Generalized Barycentric Coordinates"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Barycentric_coordinates_2/doc/Barycentric_coordinates_2/ \ 
-                              ${CMAKE_SOURCE_DIR}/Barycentric_coordinates_2/include
-
 EXTRACT_ALL                =  false
 HIDE_UNDOC_MEMBERS         =  true
 HIDE_UNDOC_CLASSES         =  true
diff --git a/Convex_decomposition_3/doc/Convex_decomposition_3/Doxyfile.in b/Convex_decomposition_3/doc/Convex_decomposition_3/Doxyfile.in
index e2046bdd84e..1a895b51d62 100644
--- a/Convex_decomposition_3/doc/Convex_decomposition_3/Doxyfile.in
+++ b/Convex_decomposition_3/doc/Convex_decomposition_3/Doxyfile.in
@@ -1,9 +1,5 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Convex Decomposition of Polyhedra"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Convex_decomposition_3/include \ 
-                              ${CMAKE_SOURCE_DIR}/Convex_decomposition_3/doc/Convex_decomposition_3/
-
 EXTRACT_ALL                =  false
 HIDE_UNDOC_CLASSES         =  true
diff --git a/Documentation/doc/CMakeLists.txt b/Documentation/doc/CMakeLists.txt
index 9833addbdfa..07f7706d946 100644
--- a/Documentation/doc/CMakeLists.txt
+++ b/Documentation/doc/CMakeLists.txt
@@ -21,10 +21,14 @@ endmacro()
 
 function(configure_doxygen_package CGAL_PACKAGE_NAME)
   if(CGAL_BRANCH_BUILD)
-    set(CGAL_PACKAGE_DOC_DIR ${CMAKE_SOURCE_DIR}/${CGAL_PACKAGE_NAME}/doc/${CGAL_PACKAGE_NAME})
+    set(CGAL_PACKAGE_DIR ${CMAKE_SOURCE_DIR}/${CGAL_PACKAGE_NAME})
   else()
-    set(CGAL_PACKAGE_DOC_DIR ${CMAKE_SOURCE_DIR}/doc/${CGAL_PACKAGE_NAME})
+    set(CGAL_PACKAGE_DIR ${CMAKE_SOURCE_DIR})
   endif()
+
+  set(CGAL_PACKAGE_DOC_DIR ${CGAL_PACKAGE_DIR}/doc/${CGAL_PACKAGE_NAME})
+  set(CGAL_PACKAGE_INCLUDE_DIR ${CGAL_PACKAGE_DIR}/include/)
+
   if(NOT IS_DIRECTORY ${CGAL_PACKAGE_DOC_DIR})
     message(STATUS "${CGAL_PACKAGE_NAME} reported but has no doc dir: ${CGAL_PACKAGE_DOC_DIR}")
     return()
@@ -32,7 +36,6 @@ function(configure_doxygen_package CGAL_PACKAGE_NAME)
     message(STATUS "Configuring documentation of ${CGAL_PACKAGE_NAME}")
   endif()
 
-  set(CGAL_PACKAGE_DIR ${CMAKE_SOURCE_DIR}/${CGAL_PACKAGE_NAME})
   if(EXISTS ${CGAL_PACKAGE_DOC_DIR}/Doxyfile.in)
     set(CGAL_DOC_PACKAGE_DEFAULTS ${CGAL_DOC_DXY_DIR}/${CGAL_PACKAGE_NAME}_defaults.dxy)
     file(REMOVE ${CGAL_DOC_PACKAGE_DEFAULTS})
@@ -60,6 +63,19 @@ function(configure_doxygen_package CGAL_PACKAGE_NAME)
     file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "ALIASES += \"cgalPkgDescriptionBegin{2}=\\details \"\n")
     file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "ALIASES += \"cgalPkgManuals{2}=<BR>\"\n")
     file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "INPUT = ${CGAL_PACKAGE_DOC_DIR}\n")
+    if(NOT EXISTS "${CGAL_PACKAGE_DOC_DIR}/CGAL")
+      # This package has in-source documentation.
+      if(CGAL_BRANCH_BUILD) # use the entire include subdir
+        file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "INPUT += ${CGAL_PACKAGE_DIR}/include/\n")
+      else() # use the filelist
+        if(EXITS "${CGAL_PACKAGE_DOC_DIR}/filelist.txt")
+          file(STRINGS "${CGAL_PACKAGE_DOC_DIR}/filelist.txt" CGAL_PKG_FILES)
+          foreach(pkg_file ${CGAL_PKG_FILES})
+            file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "INPUT += ${CGAL_PACKAGE_DIR}/include/${pkg_file}\n")
+          endforeach()
+        endif()
+      endif()
+    endif()
 
     # IMAGE_PATH is set by default. For Documentation, we generate the extra path using packages.txt
     set(IMAGE_PATH_VALUES "IMAGE_PATH = ${CGAL_PACKAGE_DOC_DIR}/fig")
diff --git a/Minkowski_sum_3/doc/Minkowski_sum_3/Doxyfile.in b/Minkowski_sum_3/doc/Minkowski_sum_3/Doxyfile.in
index 5c3086f4ae9..b2c43276148 100644
--- a/Minkowski_sum_3/doc/Minkowski_sum_3/Doxyfile.in
+++ b/Minkowski_sum_3/doc/Minkowski_sum_3/Doxyfile.in
@@ -1,10 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - 3D Minkowski Sum of Polyhedra"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Minkowski_sum_3/doc/Minkowski_sum_3/ \ 
-                              ${CMAKE_SOURCE_DIR}/Minkowski_sum_3/include/
-
 HIDE_UNDOC_MEMBERS         =  true
 HIDE_UNDOC_CLASSES         =  true
 EXTRACT_ALL                =  false
diff --git a/Point_set_processing_3/doc/Point_set_processing_3/Doxyfile.in b/Point_set_processing_3/doc/Point_set_processing_3/Doxyfile.in
index da2c4b80fba..fd2c4e4df3a 100644
--- a/Point_set_processing_3/doc/Point_set_processing_3/Doxyfile.in
+++ b/Point_set_processing_3/doc/Point_set_processing_3/Doxyfile.in
@@ -1,10 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Point Set Processing"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Point_set_processing_3/doc/Point_set_processing_3/ \ 
-                              ${CMAKE_SOURCE_DIR}/Point_set_processing_3/include
-
 EXCLUDE_PATTERNS          +=  property_map.h
 
             
diff --git a/Point_set_shape_detection_3/doc/Point_set_shape_detection_3/Doxyfile.in b/Point_set_shape_detection_3/doc/Point_set_shape_detection_3/Doxyfile.in
index b30fa491d82..1eec3a9a1f8 100644
--- a/Point_set_shape_detection_3/doc/Point_set_shape_detection_3/Doxyfile.in
+++ b/Point_set_shape_detection_3/doc/Point_set_shape_detection_3/Doxyfile.in
@@ -1,9 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME               =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Point Set Shape Detection"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Point_set_shape_detection_3/doc/Point_set_shape_detection_3/ \ 
-                              ${CMAKE_SOURCE_DIR}/Point_set_shape_detection_3/include/
 EXTRACT_ALL                =  NO
 HIDE_UNDOC_CLASSES         =  YES
 WARN_IF_UNDOCUMENTED       =  NO
diff --git a/Poisson_surface_reconstruction_3/doc/Poisson_surface_reconstruction_3/Doxyfile.in b/Poisson_surface_reconstruction_3/doc/Poisson_surface_reconstruction_3/Doxyfile.in
index 9e5a7ab6ce0..b6fa9d5f3d3 100644
--- a/Poisson_surface_reconstruction_3/doc/Poisson_surface_reconstruction_3/Doxyfile.in
+++ b/Poisson_surface_reconstruction_3/doc/Poisson_surface_reconstruction_3/Doxyfile.in
@@ -1,9 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Poisson Surface Reconstruction"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Poisson_surface_reconstruction_3/doc/Poisson_surface_reconstruction_3/ \ 
-                              ${CMAKE_SOURCE_DIR}/Poisson_surface_reconstruction_3/include
 EXTRACT_ALL                =  false
 HIDE_UNDOC_CLASSES         =  true
 WARN_IF_UNDOCUMENTED       =  false
diff --git a/Polygon/doc/Polygon/Doxyfile.in b/Polygon/doc/Polygon/Doxyfile.in
index 5d986f524c9..5c1ed3586dd 100644
--- a/Polygon/doc/Polygon/Doxyfile.in
+++ b/Polygon/doc/Polygon/Doxyfile.in
@@ -1,10 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - 2D Polygons"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Polygon/doc/Polygon/ \ 
-                              ${CMAKE_SOURCE_DIR}/Polygon/include
-
 EXTRACT_ALL                =  false
 HIDE_UNDOC_MEMBERS         =  true
 HIDE_UNDOC_CLASSES         =  true
diff --git a/Polygon_mesh_processing/doc/Polygon_mesh_processing/Doxyfile.in b/Polygon_mesh_processing/doc/Polygon_mesh_processing/Doxyfile.in
index 2df42a81b42..94bd95323b4 100644
--- a/Polygon_mesh_processing/doc/Polygon_mesh_processing/Doxyfile.in
+++ b/Polygon_mesh_processing/doc/Polygon_mesh_processing/Doxyfile.in
@@ -1,9 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Polygon Mesh Processing"
-INPUT =  ${CMAKE_SOURCE_DIR}/Polygon_mesh_processing/doc/Polygon_mesh_processing/ \
-         ${CMAKE_SOURCE_DIR}/Polygon_mesh_processing/include
-
 # custom options for this package
 EXTRACT_ALL                =  false
 HIDE_UNDOC_CLASSES         =  true
diff --git a/Polyline_simplification_2/doc/Polyline_simplification_2/Doxyfile.in b/Polyline_simplification_2/doc/Polyline_simplification_2/Doxyfile.in
index 94284b7584c..18d36146f7e 100644
--- a/Polyline_simplification_2/doc/Polyline_simplification_2/Doxyfile.in
+++ b/Polyline_simplification_2/doc/Polyline_simplification_2/Doxyfile.in
@@ -1,10 +1,3 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - 2D Polyline Simplification"
-
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Polyline_simplification_2/doc/Polyline_simplification_2/ \
-                              ${CMAKE_SOURCE_DIR}/Polyline_simplification_2/include
-
-
-
diff --git a/Scale_space_reconstruction_3/doc/Scale_space_reconstruction_3/Doxyfile.in b/Scale_space_reconstruction_3/doc/Scale_space_reconstruction_3/Doxyfile.in
index 93d62aeb762..935661e9a1d 100644
--- a/Scale_space_reconstruction_3/doc/Scale_space_reconstruction_3/Doxyfile.in
+++ b/Scale_space_reconstruction_3/doc/Scale_space_reconstruction_3/Doxyfile.in
@@ -1,9 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME		=  "CGAL ${CGAL_CREATED_VERSION_NUM} - Scale-Space Surface Reconstruction"
-
-INPUT   		=  ${CMAKE_SOURCE_DIR}/Scale_space_reconstruction_3/
-
 EXTRACT_ALL		=  NO
 HIDE_UNDOC_CLASSES	=  YES
 HIDE_UNDOC_MEMBERS	=  YES
diff --git a/Surface_mesh/doc/Surface_mesh/Doxyfile.in b/Surface_mesh/doc/Surface_mesh/Doxyfile.in
index dd8bd11bbd7..235ac44a993 100644
--- a/Surface_mesh/doc/Surface_mesh/Doxyfile.in
+++ b/Surface_mesh/doc/Surface_mesh/Doxyfile.in
@@ -1,8 +1,5 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Surface Mesh"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Surface_mesh/doc/Surface_mesh/ \ 
-                              ${CMAKE_SOURCE_DIR}/Surface_mesh/include
 MULTILINE_CPP_IS_BRIEF = YES
 
diff --git a/Surface_mesh_parameterization/doc/Surface_mesh_parameterization/Doxyfile.in b/Surface_mesh_parameterization/doc/Surface_mesh_parameterization/Doxyfile.in
index b61681a6d4a..87a2eb706fa 100644
--- a/Surface_mesh_parameterization/doc/Surface_mesh_parameterization/Doxyfile.in
+++ b/Surface_mesh_parameterization/doc/Surface_mesh_parameterization/Doxyfile.in
@@ -1,10 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Planar Parameterization of Triangulated Surface Meshes"
-
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Surface_mesh_parameterization/doc/Surface_mesh_parameterization/ \ 
-                              ${CMAKE_SOURCE_DIR}/Surface_mesh_parameterization/include
 EXTRACT_ALL                =  false
 HIDE_UNDOC_CLASSES         =  true
 WARN_IF_UNDOCUMENTED       =  false
diff --git a/Surface_mesh_segmentation/doc/Surface_mesh_segmentation/Doxyfile.in b/Surface_mesh_segmentation/doc/Surface_mesh_segmentation/Doxyfile.in
index d9f266563ca..95e2523598c 100644
--- a/Surface_mesh_segmentation/doc/Surface_mesh_segmentation/Doxyfile.in
+++ b/Surface_mesh_segmentation/doc/Surface_mesh_segmentation/Doxyfile.in
@@ -1,9 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Triangulated Surface Mesh Segmentation"
-INPUT =  ${CMAKE_SOURCE_DIR}/Surface_mesh_segmentation/doc/Surface_mesh_segmentation/ \
-         ${CMAKE_SOURCE_DIR}/Surface_mesh_segmentation/include
-
 # custom options for this package
 EXTRACT_ALL                =  false
 HIDE_UNDOC_CLASSES         =  true
diff --git a/Surface_mesh_shortest_path/doc/Surface_mesh_shortest_path/Doxyfile.in b/Surface_mesh_shortest_path/doc/Surface_mesh_shortest_path/Doxyfile.in
index 26ac8965a67..53cc6d80006 100644
--- a/Surface_mesh_shortest_path/doc/Surface_mesh_shortest_path/Doxyfile.in
+++ b/Surface_mesh_shortest_path/doc/Surface_mesh_shortest_path/Doxyfile.in
@@ -1,8 +1,5 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 PROJECT_NAME = "CGAL ${CGAL_CREATED_VERSION_NUM} - Triangulated Surface Mesh Shortest Paths"
-INPUT        = ${CMAKE_SOURCE_DIR}/Surface_mesh_shortest_path/doc/Surface_mesh_shortest_path/ \
-               ${CMAKE_SOURCE_DIR}/Surface_mesh_shortest_path/include
-
 INTERNAL_DOCS = NO
 EXTRACT_ALL = NO
 HIDE_UNDOC_CLASSES = YES
diff --git a/Surface_mesh_skeletonization/doc/Surface_mesh_skeletonization/Doxyfile.in b/Surface_mesh_skeletonization/doc/Surface_mesh_skeletonization/Doxyfile.in
index ffc99f2601d..4ef3d555ca4 100644
--- a/Surface_mesh_skeletonization/doc/Surface_mesh_skeletonization/Doxyfile.in
+++ b/Surface_mesh_skeletonization/doc/Surface_mesh_skeletonization/Doxyfile.in
@@ -1,9 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
  
 PROJECT_NAME =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Triangulated Surface Mesh Skeletonization"
-INPUT =  ${CMAKE_SOURCE_DIR}/Surface_mesh_skeletonization/doc/Surface_mesh_skeletonization/ \ 
-         ${CMAKE_SOURCE_DIR}/Surface_mesh_skeletonization/include
-
 EXTRACT_ALL                =  false
 HIDE_UNDOC_MEMBERS         =  true
 HIDE_UNDOC_CLASSES         =  true
diff --git a/Surface_modeling/doc/Surface_modeling/Doxyfile.in b/Surface_modeling/doc/Surface_modeling/Doxyfile.in
index f441c245ad0..60850730bb8 100644
--- a/Surface_modeling/doc/Surface_modeling/Doxyfile.in
+++ b/Surface_modeling/doc/Surface_modeling/Doxyfile.in
@@ -1,10 +1,6 @@
 @INCLUDE = ${CGAL_DOC_PACKAGE_DEFAULTS}
 
 PROJECT_NAME                       =  "CGAL ${CGAL_CREATED_VERSION_NUM} - Triangulated Surface Mesh Deformation"
-
-INPUT                      =  ${CMAKE_SOURCE_DIR}/Surface_modeling/doc/Surface_modeling/ \ 
-                              ${CMAKE_SOURCE_DIR}/Surface_modeling/include
-
 EXTRACT_ALL                =  false
 HIDE_UNDOC_MEMBERS         =  true
 HIDE_UNDOC_CLASSES         =  true