diff --git a/Arrangement_on_surface_2/test/Arrangement_on_surface_2/cgal_test.cmake b/Arrangement_on_surface_2/test/Arrangement_on_surface_2/cgal_test.cmake
index 552b435d9a4..7fd18c6944b 100644
--- a/Arrangement_on_surface_2/test/Arrangement_on_surface_2/cgal_test.cmake
+++ b/Arrangement_on_surface_2/test/Arrangement_on_surface_2/cgal_test.cmake
@@ -156,6 +156,7 @@ function(cgal_arr_2_add_target exe_name source_file)
     set(name ${exe_name}_${suffix})
   endif()
   add_executable(${name} ${source_file})
+  add_to_cached_list( CGAL_EXECUTABLE_TARGETS ${name} )
   separate_arguments(flags UNIX_COMMAND "${TESTSUITE_CXXFLAGS}")
   target_compile_options(${name} PRIVATE ${flags})
   cgal_debug_message(STATUS "#      -> target ${name} with TESTSUITE_CXXFLAGS: ${flags}")
diff --git a/Installation/CMakeLists.txt b/Installation/CMakeLists.txt
index 8afc7721d61..f16e99d4a1a 100644
--- a/Installation/CMakeLists.txt
+++ b/Installation/CMakeLists.txt
@@ -957,12 +957,17 @@ endif()
 #
 #--------------------------------------------------------------------------------------------------
 
+if(NOT TARGET ALL_CGAL_TARGETS)
+  add_custom_target( ALL_CGAL_TARGETS )
+endif()
+
 macro( add_programs subdir target ON_OFF )
 
   cache_set( CGAL_EXECUTABLE_TARGETS "" )
   
   add_custom_target( ${target} )
-  
+  add_dependencies( ALL_CGAL_TARGETS ${target} )
+
   option( WITH_${target} "Select ${target}" ${ON_OFF} )
   if ( WITH_${target} )
     add_subdirectory( ${subdir} EXCLUDE_FROM_ALL )
diff --git a/Installation/cmake/modules/CGAL_add_test.cmake b/Installation/cmake/modules/CGAL_add_test.cmake
index 4e7345aeaea..fe7c45751d1 100644
--- a/Installation/cmake/modules/CGAL_add_test.cmake
+++ b/Installation/cmake/modules/CGAL_add_test.cmake
@@ -98,8 +98,12 @@ function(cgal_add_compilation_test exe_name)
     COMMAND ${TIME_COMMAND} "${CMAKE_COMMAND}" --build "${CMAKE_BINARY_DIR}" --target "${exe_name}")
   set_property(TEST "compilation_of__${exe_name}"
     APPEND PROPERTY LABELS "${PROJECT_NAME}")
+  if(NOT TARGET ALL_CGAL_TARGETS)
+    add_custom_target( ALL_CGAL_TARGETS )
+  endif()
   if(NOT TARGET cgal_check_build_system)
     add_custom_target(cgal_check_build_system)
+    add_dependencies( ALL_CGAL_TARGETS cgal_check_build_system )
   endif()
   if(NOT TEST check_build_system)
     add_test(NAME "check_build_system"
diff --git a/Installation/cmake/modules/CGAL_enable_end_of_configuration_hook.cmake b/Installation/cmake/modules/CGAL_enable_end_of_configuration_hook.cmake
index 6f8e423af1d..e0f001f0d4b 100644
--- a/Installation/cmake/modules/CGAL_enable_end_of_configuration_hook.cmake
+++ b/Installation/cmake/modules/CGAL_enable_end_of_configuration_hook.cmake
@@ -9,7 +9,7 @@
 
 get_property(PROPERTY_CGAL_run_at_the_end_of_configuration_INCLUDED
   GLOBAL PROPERTY CGAL_run_at_the_end_of_configuration_INCLUDED)
-if(PROPERTY_CGAL_run_at_the_end_of_configuration_INCLUDED)
+if(CGAL_SKIP_CMAKE_HOOKS OR PROPERTY_CGAL_run_at_the_end_of_configuration_INCLUDED)
   return()
 endif()
 
@@ -17,11 +17,38 @@ function(CGAL_run_at_the_end_of_configuration variable access value current_list
   if(NOT access STREQUAL "MODIFIED_ACCESS")
     return()
   endif()
-  if(CGAL_CHECK_UNUSED_CPP_FILES
-      AND NOT current_list_file STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt"
-      AND stack STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt")
+  if(current_list_file STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt"
+      OR NOT stack STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.txt"
+      OR stack MATCHES doc/CMakeLists.txt
+      OR stack MATCHES demo/Polyhedron/)
+    return()
+  endif()
+  get_property(_targets DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY BUILDSYSTEM_TARGETS)
+  if(CGAL_CHECK_UNREFERENCES_TARGETS)
+    set(_list_of_deps)
+    set(_special_targets  demos examples tests ALL_CGAL_TARGETS CGAL_Qt5_moc_and_resources uninstall install_FindCGAL)
+    foreach(t ${_special_targets})
+      if(NOT TARGET ${t})
+        continue()
+      endif()
+      get_property(_deps TARGET ${t} PROPERTY MANUALLY_ADDED_DEPENDENCIES)
+#      message("  deps of ${t}: ${_deps}")
+      list(APPEND _list_of_deps ${_deps})
+    endforeach()
+    list(APPEND _list_of_deps ${CGAL_EXECUTABLE_TARGETS})
+#    message(STATUS "  all deps: ${_list_of_deps}")
+    foreach(target ${_targets})
+#      message(STATUS "  new target: ${target}")
+      if(${target} IN_LIST _special_targets)
+        continue()
+      endif()
+      if(NOT ${target} IN_LIST _list_of_deps)
+        message(AUTHOR_WARNING "  orphan target: ${target}")
+      endif()
+    endforeach()
+  endif()
+  if(CGAL_CHECK_UNUSED_CPP_FILES)
     file(GLOB _cppfiles ${CMAKE_CURRENT_SOURCE_DIR}/*.cpp)
-    get_property(_targets DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY BUILDSYSTEM_TARGETS)
     if(_targets AND _cppfiles)
       set(_sources)
       foreach(_target ${_targets})
diff --git a/Installation/src/CMakeLists.txt b/Installation/src/CMakeLists.txt
index 09db484fd6e..7ed919fab92 100644
--- a/Installation/src/CMakeLists.txt
+++ b/Installation/src/CMakeLists.txt
@@ -72,7 +72,10 @@ function (collect_cgal_library LIBRARY_NAME ADDITIONAL_FILES)
   # CMakeLists.txt can be the target like if it was an imported
   # target.
   add_library(CGAL::${LIBRARY_NAME} ALIAS ${LIBRARY_NAME})
-
+  if(NOT TARGET ALL_CGAL_TARGETS)
+    add_custom_target( ALL_CGAL_TARGETS )
+  endif()
+  add_dependencies( ALL_CGAL_TARGETS ${LIBRARY_NAME} )
   if(CGAL_AUTO_LINK_ENABLED)
     if (NOT CGAL_HEADER_ONLY)
       set_target_properties( ${LIBRARY_NAME} PROPERTIES
diff --git a/Installation/test/Installation/CMakeLists.txt b/Installation/test/Installation/CMakeLists.txt
index 1428689fa6b..bf473a7d7cb 100644
--- a/Installation/test/Installation/CMakeLists.txt
+++ b/Installation/test/Installation/CMakeLists.txt
@@ -23,7 +23,9 @@ macro(create_link_to_program COMPONENT )
   else()
     target_link_libraries(link_to_${COMPONENT} CGAL::${COMPONENT} ${CGAL_3RD_PARTY_LIBRARIES} ${${COMPONENT}_3RD_PARTY_LIBRARIES} )
   endif()
-  
+
+  add_to_cached_list( CGAL_EXECUTABLE_TARGETS link_to_${COMPONENT} )
+
 endmacro()
 
 find_package(CGAL QUIET COMPONENTS Core)
@@ -82,6 +84,7 @@ if ( CGAL_FOUND )
     add_executable(test_gmp_mpfr_dll test_gmp_mpfr_dll.cpp)
     target_link_libraries(test_gmp_mpfr_dll version)
     CGAL_add_test(test_gmp_mpfr_dll)
+    add_to_cached_list( CGAL_EXECUTABLE_TARGETS test_gmp_mpfr_dll )
   endif()
 
   find_package( LEDA QUIET)
diff --git a/Mesh_3/examples/Mesh_3/CMakeLists.txt b/Mesh_3/examples/Mesh_3/CMakeLists.txt
index 028d1217f04..dcaedc3629a 100644
--- a/Mesh_3/examples/Mesh_3/CMakeLists.txt
+++ b/Mesh_3/examples/Mesh_3/CMakeLists.txt
@@ -94,6 +94,7 @@ if ( CGAL_FOUND )
         add_executable ( mesh_3D_gray_vtk_image mesh_3D_gray_vtk_image.cpp )
         target_link_libraries(  mesh_3D_gray_vtk_image ${CGAL_LIBRARIES} ${CGAL_3RD_PARTY_LIBRARIES} ${VTK_LIBRARIES})
         cgal_add_test( mesh_3D_gray_vtk_image )
+        add_to_cached_list( CGAL_EXECUTABLE_TARGETS mesh_3D_gray_vtk_image )
       endif()
  
       create_single_source_cgal_program( "mesh_3D_gray_image.cpp" )
diff --git a/Polyhedron/demo/Polyhedron/CMakeLists.txt b/Polyhedron/demo/Polyhedron/CMakeLists.txt
index 313305843f9..866dcf9f74f 100644
--- a/Polyhedron/demo/Polyhedron/CMakeLists.txt
+++ b/Polyhedron/demo/Polyhedron/CMakeLists.txt
@@ -230,6 +230,7 @@ if(CGAL_Qt5_FOUND AND Qt5_FOUND)
       PUBLIC demo_framework ${CGAL_LIBRARIES}
       Qt5::OpenGL Qt5::Gui Qt5::Script Qt5::Widgets)
     cgal_add_compilation_test(${item_name})
+    add_to_cached_list( CGAL_EXECUTABLE_TARGETS ${item_name} )
   endmacro(add_item)
 
   add_item(scene_c3t3_item Scene_c3t3_item.cpp)