diff --git a/CHANGES b/CHANGES
index bdde1063..119c1f3c 100644
--- a/CHANGES
+++ b/CHANGES
@@ -6,6 +6,7 @@ What's New for OpenJPEG
 + : added
 
 April 13, 2011
+! [antonin] changed the directory hierarchy of the whole project. See README files for details.
 ! [antonin] moved "openjpeg3d" directory from the trunk to the branches directory.
 ! [antonin] renamed and reorganized "jp3d" directory to "openjpeg3d". Is now a standalone directory, with independent cmake files. Done as it uses its own version of the openjpeg library and does not depend on the one currently developped. Will be removed from the trunk and stored in a branch.
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4c5c79a1..474a5f02 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -38,12 +38,6 @@ SET(OPENJPEG_LIBRARY_PROPERTIES
   VERSION   "${OPENJPEG_VERSION_MAJOR}.${OPENJPEG_VERSION_MINOR}.${OPENJPEG_VERSION_BUILD}"
   SOVERSION "${OPENJPEG_VERSION_MAJOR}"
 )
-# You will also need to define a value for the following variables:
-# OPENJPEG_INSTALL_BIN_DIR          - binary dir (executables)
-# OPENJPEG_INSTALL_LIB_DIR          - library dir (libs)
-# OPENJPEG_INSTALL_DATA_DIR         - share dir (say, examples, data, etc)
-# OPENJPEG_INSTALL_INCLUDE_DIR      - include dir (headers)
-
 
 # On Visual Studio 8 MS deprecated C. This removes all 1.276E1265 security
 # warnings
@@ -75,7 +69,7 @@ ENDIF(WIN32)
 # Install directories
 
 STRING(TOLOWER ${PROJECT_NAME} projectname)
-SET(subdir "${projectname}-${OPENJPEG_VERSION_MAJOR}.${OPENJPEG_VERSION_MINOR}")
+SET(OPENJPEG_INSTALL_SUBDIR "${projectname}-${OPENJPEG_VERSION_MAJOR}.${OPENJPEG_VERSION_MINOR}")
 
 IF(NOT OPENJPEG_INSTALL_BIN_DIR)
   SET(OPENJPEG_INSTALL_BIN_DIR "bin")
@@ -86,7 +80,7 @@ IF(NOT OPENJPEG_INSTALL_LIB_DIR)
 ENDIF(NOT OPENJPEG_INSTALL_LIB_DIR)
 
 IF(NOT OPENJPEG_INSTALL_DATA_DIR)
-  SET(OPENJPEG_INSTALL_DATA_DIR "share/${subdir}")
+  SET(OPENJPEG_INSTALL_DATA_DIR "share/${OPENJPEG_INSTALL_SUBDIR}")
 ENDIF(NOT OPENJPEG_INSTALL_DATA_DIR)
 
 IF(NOT OPENJPEG_INSTALL_INCLUDE_DIR)
@@ -98,11 +92,11 @@ IF(NOT OPENJPEG_INSTALL_MAN_DIR)
 ENDIF(NOT OPENJPEG_INSTALL_MAN_DIR)
 
 IF(NOT OPENJPEG_INSTALL_DOC_DIR)
-  SET(OPENJPEG_INSTALL_DOC_DIR "share/doc/${subdir}")
+  SET(OPENJPEG_INSTALL_DOC_DIR "share/doc/${OPENJPEG_INSTALL_SUBDIR}")
 ENDIF(NOT OPENJPEG_INSTALL_DOC_DIR)
 
 IF(NOT OPENJPEG_INSTALL_PACKAGE_DIR)
-  SET(OPENJPEG_INSTALL_PACKAGE_DIR ${OPENJPEG_INSTALL_LIB_DIR}/${subdir}
+  SET(OPENJPEG_INSTALL_PACKAGE_DIR ${OPENJPEG_INSTALL_LIB_DIR}/${OPENJPEG_INSTALL_SUBDIR}
     CACHE INTERNAL "")
 ENDIF(NOT OPENJPEG_INSTALL_PACKAGE_DIR)
 
@@ -112,26 +106,24 @@ INCLUDE (${CMAKE_ROOT}/Modules/CMakeBackwardCompatibilityC.cmake)
 
 #-----------------------------------------------------------------------------
 # Test for getopt being available in this system
-INCLUDE (${PROJECT_SOURCE_DIR}/CMake/CheckHaveGetopt.cmake )
+INCLUDE (${OPENJPEG_SOURCE_DIR}/CMake/CheckHaveGetopt.cmake )
 
 #-----------------------------------------------------------------------------
 # Setup file for setting custom ctest vars
 CONFIGURE_FILE(
-  ${CMAKE_CURRENT_SOURCE_DIR}/CMake/CTestCustom.cmake.in
-  ${CMAKE_CURRENT_BINARY_DIR}/CTestCustom.cmake
+  ${CMAKE_SOURCE_DIR}/testing/CTestCustom.cmake.in
+  ${CMAKE_BINARY_DIR}/testing/CTestCustom.cmake
   @ONLY
   )
 
 #-----------------------------------------------------------------------------
 # OpenJPEG build configuration options.
 OPTION(BUILD_SHARED_LIBS "Build OpenJPEG shared library and link executables against it." ON)
-
-#-----------------------------------------------------------------------------
 SET (EXECUTABLE_OUTPUT_PATH ${OPENJPEG_BINARY_DIR}/bin CACHE PATH "Single output directory for building all executables.")
 SET (LIBRARY_OUTPUT_PATH ${OPENJPEG_BINARY_DIR}/bin CACHE PATH "Single output directory for building all libraries.")
 MARK_AS_ADVANCED(LIBRARY_OUTPUT_PATH EXECUTABLE_OUTPUT_PATH)
 
-
+#-----------------------------------------------------------------------------
 # configure name mangling to allow multiple libraries to coexist
 # peacefully
 IF(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/openjpeg_mangle.h.in)
@@ -148,50 +140,6 @@ INSTALL( FILES  ${CMAKE_CURRENT_BINARY_DIR}/libopenjpeg1.pc DESTINATION ${OPENJP
 INSTALL( CODE
   "EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E create_symlink \"libopenjpeg1.pc\" \"\$ENV{DESTDIR}${OPENJPEG_INSTALL_LIB_DIR}/pkgconfig/libopenjpeg.pc\")")
 
-#-----------------------------------------------------------------------------
-# Always build the library
-INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR})
-SUBDIRS(libopenjpeg)
-
-#-----------------------------------------------------------------------------
-# Build CODEC executables ?
-OPTION(BUILD_CODEC "Build the CODEC executables" ON)
-
-#-----------------------------------------------------------------------------
-# Build MJ2 executables ?
-OPTION(BUILD_MJ2 "Build the MJ2 executables." OFF)
-
-#-----------------------------------------------------------------------------
-# Build JPWL executables ?
-OPTION(BUILD_JPWL "Build the JPWL executables" OFF)
-
-#-----------------------------------------------------------------------------
-# Build INDEXER_JPIP executables ?
-OPTION(BUILD_INDEXER_JPIP "Build the INDEXER_JPIP executables" OFF)
-
-#-----------------------------------------------------------------------------
-# Build DOCUMENTATION ?
-OPTION(BUILD_DOC "Build the doxygen documentation" OFF)
-
-#-----------------------------------------------------------------------------
-# For openjpeg team if they ever want CDash+CMake
-OPTION(BUILD_TESTING "Build the tests." OFF)
-IF(BUILD_TESTING)
-  ENABLE_TESTING()
-  INCLUDE(CTest)
-ENDIF(BUILD_TESTING)
-
-# Adding test with dataset from:
-# http://www.crc.ricoh.com/~gormish/jpeg2000conformance/
-# -> wget http://www.crc.ricoh.com/~gormish/jpeg2000conformance/j2kp4files_v1_5.zip
-# http://www.jpeg.org/jpeg2000guide/testimages/testimages.html
-#-----------------------------------------------------------------------------
-# Adding JPEG2000_CONFORMANCE_DATA_ROOT
-FIND_PATH(JPEG2000_CONFORMANCE_DATA_ROOT testimages.html
-  ${OPENJPEG_SOURCE_DIR}/../jpeg2000testimages
-  $ENV{JPEG2000_CONFORMANCE_DATA_ROOT}
-)
-
 #-----------------------------------------------------------------------------
 # Compiler specific flags:
 IF(CMAKE_COMPILER_IS_GNUCC)
@@ -201,21 +149,8 @@ IF(CMAKE_COMPILER_IS_GNUCC)
   SET(CMAKE_C_FLAGS_RELEASE "-ffast-math ${CMAKE_C_FLAGS_RELEASE}")
 ENDIF(CMAKE_COMPILER_IS_GNUCC)
 
-# install all targets referenced as OPENJPEGTargets
-install(EXPORT OpenJPEGTargets DESTINATION ${OPENJPEG_INSTALL_PACKAGE_DIR})
-CONFIGURE_FILE( ${OPENJPEG_SOURCE_DIR}/CMake/OpenJPEGConfig.cmake.in
-  ${OPENJPEG_BINARY_DIR}/OpenJPEGConfig.cmake
-  @ONLY
-)
-INSTALL( FILES ${OPENJPEG_BINARY_DIR}/OpenJPEGConfig.cmake
-  DESTINATION ${OPENJPEG_INSTALL_PACKAGE_DIR}
-)
-# install CHANGES and LICENSE
-INSTALL(
-  FILES       CHANGES 
-              LICENSE
-  DESTINATION ${OPENJPEG_INSTALL_DOC_DIR})
-#
+#-----------------------------------------------------------------------------
+# opj_config.h generation
 FIND_FILE(HAVE_STRINGS_H_FOUND strings.h)
 IF(NOT HAVE_STRINGS_H_FOUND STREQUAL "HAVE_STRINGS_H_FOUND-NOTFOUND")
   FIND_FILE(HAVE_STRINGS_H strings.h)
@@ -261,151 +196,65 @@ IF(NOT HAVE_UNISTD_H_FOUND STREQUAL "HAVE_UNISTD_H_FOUND-NOTFOUND")
   FIND_FILE(HAVE_UNISTD_H unistd.h)
   SET(HAS_UNISTD_H 1)
 ENDIF()
-#
-IF(BUILD_CODEC OR BUILD_JPWL OR BUILD_MJ2)
-#
-#
-IF(UNIX OR CYGWIN)
- SET(CMAKE_INCLUDE_PATH /usr/include /usr/local/include /opt/include 
-	/opt/local/include /usr/include/libpng /usr/include/libpng14
-	/usr/include/libpng12 /usr/local/include/libpng 
-	/usr/local/include/libpng14 /usr/local/include/libpng12
-	/opt/include/libpng /opt/include/libpng14 /opt/include/libpng12
-	/opt/local/include/libpng /opt/local/include/libpng14)
- SET(CMAKE_LIBRARY_PATH /usr/lib /usr/local/lib /opt/lib /opt/local/lib)
-ENDIF()
-#
- FIND_PACKAGE(ZLIB)
-#
- IF(ZLIB_LIBRARY STREQUAL "ZLIB_LIBRARY-NOTFOUND")
-   SET(ZLIB_FOUND 0)
- ENDIF(ZLIB_LIBRARY STREQUAL "ZLIB_LIBRARY-NOTFOUND")
-#
- IF(ZLIB_FOUND)
-   SET(HAVE_ZLIB_H 1)
-   SET(HABE_LIBZ 1)
-   SET(Z_LIBNAME ${ZLIB_LIBRARIES})
-   SET(Z_INCLUDE_DIRNAME ${ZLIB_INCLUDE_DIR}) 
- ENDIF(ZLIB_FOUND)
-#
- FIND_PACKAGE(PNG)
-#
- IF(PNG_LIBRARY STREQUAL "PNG_LIBRARY-NOTFOUND")
-   SET(PNG_FOUND 0)
- ENDIF(PNG_LIBRARY STREQUAL "PNG_LIBRARY-NOTFOUND")
-#
- IF(PNG_FOUND)
-   SET(HAVE_PNG_H 1)
-   SET(HAVE_LIBPNG 1)
-   SET(PNG_LIBNAME ${PNG_LIBRARIES})
-   SET(PNG_INCLUDE_DIRNAME ${PNG_INCLUDE_DIR})
- ENDIF(PNG_FOUND)
-#
- FIND_PACKAGE(TIFF)
-#
- IF(TIFF_LIBRARY STREQUAL "TIFF_LIBRARY-NOTFOUND")
-   SET(TIFF_FOUND 0)
- ENDIF(TIFF_LIBRARY STREQUAL "TIFF_LIBRARY-NOTFOUND")
-#
- IF(TIFF_FOUND)
-   SET(HAVE_TIFF_H 1)
-   SET(HAVE_LIBTIFF 1)
-   SET(TIFF_LIBNAME ${TIFF_LIBRARIES})
-   SET(TIFF_INCLUDE_DIRNAME ${TIFF_INCLUDE_DIR})
- ENDIF(TIFF_FOUND)
-#
- SET(LCMS12_MISSING 1)
- INCLUDE(thirdparty/FindLCMS2.cmake OPTIONAL)
-#
- IF(LCMS2_FOUND)
-  SET(LCMS12_MISSING 0)
-  SET(HAVE_LCMS2_H 1)
-  SET(HAVE_LIBLCMS2 1)
-  SET(LCMS_LIBNAME ${LCMS2_LIBRARY})
-  SET(LCMS_INCLUDE_DIRNAME ${LCMS2_INCLUDE_DIR})
- ENDIF(LCMS2_FOUND)
-#
- IF(NOT LCMS2_FOUND)
-  INCLUDE(thirdparty/FindLCMS.cmake OPTIONAL)
-#
-  IF(LCMS_FOUND)
-   SET(LCMS12_MISSING 0)
-   SET(HAVE_LCMS1_H 1)
-    SET(HAVE_LIBLCMS1 1)
-    SET(LCMS_LIBNAME ${LCMS_LIBRARY} )
-    SET(LCMS_INCLUDE_DIRNAME ${LCMS_INCLUDE_DIR})
-  ENDIF(LCMS_FOUND)
- ENDIF(NOT LCMS2_FOUND)
-#-------------------------------------------------------------
- OPTION(BUILD_THIRDPARTY "Build the thirdparty executables" ON)
-#
- IF(NOT ZLIB_FOUND OR NOT PNG_FOUND OR NOT TIFF_FOUND OR LCMS12_MISSING) 
-  IF(BUILD_THIRDPARTY)
-   SET(HAVE_ZLIB_H 1)
-   SET(HAVE_LIBZ 1)
-   SET(HAVE_PNG_H 1)
-   SET(HAVE_LIBPNG 1)
-   SET(HAVE_TIFF_H 1)
-   SET(HAVE_LIBTIFF 1)
-   SET(HAVE_LCMS2_H 1)
-   SET(HAVE_LIBLCMS2 1)
-#
-   ADD_SUBDIRECTORY(${OPENJPEG_SOURCE_DIR}/thirdparty)
-#
-   LINK_DIRECTORIES(${CMAKE_BINARY_DIR}/thirdparty/lib)
-#
-   IF(NOT ZLIB_FOUND)
-    INCLUDE_DIRECTORIES(${OPENJPEG_SOURCE_DIR}/thirdparty/include)
-    SET(ZLIB_INCLUDE_DIRNAME ${OPENJPEG_SOURCE_DIR}/thirdparty/include)
-    SET(Z_LIBNAME z)
-    SET(ZLIB_FOUND 1)
-   ENDIF(NOT ZLIB_FOUND)
-#
-   IF(NOT PNG_FOUND)
-    SET(PNG_INCLUDE_DIRNAME ${OPENJPEG_SOURCE_DIR}/thirdparty/libpng)
-    SET(PNG_LIBNAME png)
-    SET(PNG_FOUND 1)
-   ENDIF(NOT PNG_FOUND)
-#
-   IF(NOT LCMS_FOUND AND NOT LCMS2_FOUND)
-    SET(LCMS_INCLUDE_DIRNAME ${OPENJPEG_SOURCE_DIR}/thirdparty/liblcms2/include)
-    SET(LCMS_LIBNAME lcms2)
-    SET(LCMS2_FOUND 1)
-   ENDIF(NOT LCMS_FOUND AND NOT LCMS2_FOUND)
-#
-   IF(NOT TIFF_FOUND)
-    SET(TIFF_INCLUDE_DIRNAME ${OPENJPEG_SOURCE_DIR}/thirdparty/libtiff)
-    SET(TIFF_LIBNAME tiff)
-    SET(TIFF_FOUND 1)
-   ENDIF(NOT TIFF_FOUND)
-#
-  ENDIF(BUILD_THIRDPARTY)
- ENDIF(NOT ZLIB_FOUND OR NOT PNG_FOUND OR NOT TIFF_FOUND OR LCMS12_MISSING)
-#
-ENDIF(BUILD_CODEC OR BUILD_JPWL OR BUILD_MJ2)
-#
-IF(BUILD_CODEC)
- SUBDIRS(codec)
-ENDIF(BUILD_CODEC)
-#
-IF(BUILD_MJ2)
- SUBDIRS(mj2)
-ENDIF(BUILD_MJ2)
-#
-IF(BUILD_JPWL)
- SUBDIRS(jpwl)
-ENDIF(BUILD_JPWL)
-#
-IF(BUILD_INDEXER_JPIP)
- SUBDIRS(indexer_JPIP)
-ENDIF(BUILD_INDEXER_JPIP)
-#
-IF(BUILD_DOC)
- SUBDIRS(doc)
-ENDIF(BUILD_DOC)
-#
-# generate opj_config.h
 CONFIGURE_FILE("${OPENJPEG_SOURCE_DIR}/opj_configh.cmake.in"
  "${OPENJPEG_BINARY_DIR}/opj_config.h"
- @ONLY 
+ @ONLY
+ )
+
+#-----------------------------------------------------------------------------
+# Build Library
+INCLUDE_DIRECTORIES(BEFORE ${OPENJPEG_BINARY_DIR})
+ADD_SUBDIRECTORY(libopenjpeg)
+
+#-----------------------------------------------------------------------------
+# Build Applications
+OPTION(BUILD_CODEC "Build the CODEC executables" ON)
+OPTION(BUILD_MJ2 "Build the MJ2 executables." OFF)
+OPTION(BUILD_INDEXER_JPIP "Build the INDEXER_JPIP executables" OFF)
+ADD_SUBDIRECTORY(applications)
+
+#-----------------------------------------------------------------------------
+# Build JPWL-flavoured library and executables
+OPTION(BUILD_JPWL "Build the JPWL library and executables" OFF)
+
+#-----------------------------------------------------------------------------
+# Build DOCUMENTATION
+OPTION(BUILD_DOC "Build the doxygen documentation" OFF)
+IF(BUILD_DOC)
+ ADD_SUBDIRECTORY(doc)
+ENDIF(BUILD_DOC)
+
+#-----------------------------------------------------------------------------
+# CDash+CMake : to be updated
+OPTION(BUILD_TESTING "Build the tests." OFF)
+IF(BUILD_TESTING)
+  ENABLE_TESTING()
+  INCLUDE(CTest)
+ENDIF(BUILD_TESTING)
+# Adding test with dataset from:
+# http://www.crc.ricoh.com/~gormish/jpeg2000conformance/
+# -> wget http://www.crc.ricoh.com/~gormish/jpeg2000conformance/j2kp4files_v1_5.zip
+# http://www.jpeg.org/jpeg2000guide/testimages/testimages.html
+# Adding JPEG2000_CONFORMANCE_DATA_ROOT
+FIND_PATH(JPEG2000_CONFORMANCE_DATA_ROOT testimages.html
+  ${OPENJPEG_SOURCE_DIR}/../jpeg2000testimages
+  $ENV{JPEG2000_CONFORMANCE_DATA_ROOT}
 )
+
+#-----------------------------------------------------------------------------
+# install all targets referenced as OPENJPEGTargets
+INSTALL(EXPORT OpenJPEGTargets DESTINATION ${OPENJPEG_INSTALL_PACKAGE_DIR})
+CONFIGURE_FILE( ${OPENJPEG_SOURCE_DIR}/CMake/OpenJPEGConfig.cmake.in
+  ${OPENJPEG_BINARY_DIR}/OpenJPEGConfig.cmake
+  @ONLY
+)
+INSTALL( FILES ${OPENJPEG_BINARY_DIR}/OpenJPEGConfig.cmake
+  DESTINATION ${OPENJPEG_INSTALL_PACKAGE_DIR}
+)
+
+#-----------------------------------------------------------------------------
+# install CHANGES and LICENSE
+INSTALL(
+  FILES       CHANGES 
+              LICENSE
+  DESTINATION ${OPENJPEG_INSTALL_DOC_DIR})
diff --git a/CTestCustom.cmake.in b/CTestCustom.cmake.in
deleted file mode 100644
index 00ad6670..00000000
--- a/CTestCustom.cmake.in
+++ /dev/null
@@ -1,21 +0,0 @@
-#
-# For further details regarding this file, 
-# see http://www.vtk.org/Wiki/CMake_Testing_With_CTest#Customizing_CTest
-#
-
-SET (CTEST_CUSTOM_MAXIMUM_NUMBER_OF_ERRORS   50)
-SET (CTEST_CUSTOM_MAXIMUM_NUMBER_OF_WARNINGS 50)
-
-SET(CTEST_CUSTOM_COVERAGE_EXCLUDE
- ${CTEST_CUSTOM_COVERAGE_EXCLUDE}
-
- # Exclude files from the Testing directories
- ".*/Testing/.*"
- )
-
-SET(CTEST_CUSTOM_WARNING_EXCEPTION
-  ${CTEST_CUSTOM_WARNING_EXCEPTION}
-  
-  # Suppress warning caused by intentional messages about deprecation
-  ".*warning,.* is deprecated"
-)
diff --git a/README b/README
index 031cf3d8..2ee2b541 100644
--- a/README
+++ b/README
@@ -1 +1,23 @@
+
+OPENJPEG LIBRARY and APPLICATIONS
+----------------------------------
+
+Details on folders hierarchy:
+
+* libopenjpeg: contains the sources of the openjpeg library
+    * jpwl: contains the additional sources if you want to build a JPWL-flavoured library.
+* applications: contains all applications that use the openjpeg library
+    * common: common files to all applications
+    * codec: a basic codec
+    * mj2: motion jpeg 2000 executables
+    * JavaOpenJPEG: java jni to use openjpeg in a java program
+    * indexer_JPIP: obsolete. Will be replaced by a complete JPIP implementation soon.
+    * OPJViewer: gui for displaying j2k files (based on wxWidget)
+* thirdparty: thirdparty libraries used by some applications. These libraries will be build only if there are not found on the system. Note that libopenjpeg itself does not have any dependency.
+* doc: doxygen documentation setup file and man pages
+* testing: all files required to test the library and executables (obsolete)
+* CMake: cmake related files
+* m4: autotools related files
+
+see LICENSE for license and copyright information
 see INSTALL for installation procedures.
\ No newline at end of file
diff --git a/applications/CMakeLists.txt b/applications/CMakeLists.txt
new file mode 100644
index 00000000..f4f16e4b
--- /dev/null
+++ b/applications/CMakeLists.txt
@@ -0,0 +1,134 @@
+IF(BUILD_CODEC OR BUILD_MJ2)
+#
+#
+IF(UNIX OR CYGWIN)
+ SET(CMAKE_INCLUDE_PATH /usr/include /usr/local/include /opt/include 
+	/opt/local/include /usr/include/libpng /usr/include/libpng14
+	/usr/include/libpng12 /usr/local/include/libpng 
+	/usr/local/include/libpng14 /usr/local/include/libpng12
+	/opt/include/libpng /opt/include/libpng14 /opt/include/libpng12
+	/opt/local/include/libpng /opt/local/include/libpng14)
+ SET(CMAKE_LIBRARY_PATH /usr/lib /usr/local/lib /opt/lib /opt/local/lib)
+ENDIF()
+#
+ FIND_PACKAGE(ZLIB)
+#
+ IF(ZLIB_LIBRARY STREQUAL "ZLIB_LIBRARY-NOTFOUND")
+   SET(ZLIB_FOUND 0)
+ ENDIF(ZLIB_LIBRARY STREQUAL "ZLIB_LIBRARY-NOTFOUND")
+#
+ IF(ZLIB_FOUND)
+   SET(HAVE_ZLIB_H 1)
+   SET(HABE_LIBZ 1)
+   SET(Z_LIBNAME ${ZLIB_LIBRARIES})
+   SET(Z_INCLUDE_DIRNAME ${ZLIB_INCLUDE_DIR}) 
+ ENDIF(ZLIB_FOUND)
+#
+ FIND_PACKAGE(PNG)
+#
+ IF(PNG_LIBRARY STREQUAL "PNG_LIBRARY-NOTFOUND")
+   SET(PNG_FOUND 0)
+ ENDIF(PNG_LIBRARY STREQUAL "PNG_LIBRARY-NOTFOUND")
+#
+ IF(PNG_FOUND)
+   SET(HAVE_PNG_H 1)
+   SET(HAVE_LIBPNG 1)
+   SET(PNG_LIBNAME ${PNG_LIBRARIES})
+   SET(PNG_INCLUDE_DIRNAME ${PNG_INCLUDE_DIR})
+ ENDIF(PNG_FOUND)
+#
+ FIND_PACKAGE(TIFF)
+#
+ IF(TIFF_LIBRARY STREQUAL "TIFF_LIBRARY-NOTFOUND")
+   SET(TIFF_FOUND 0)
+ ENDIF(TIFF_LIBRARY STREQUAL "TIFF_LIBRARY-NOTFOUND")
+#
+ IF(TIFF_FOUND)
+   SET(HAVE_TIFF_H 1)
+   SET(HAVE_LIBTIFF 1)
+   SET(TIFF_LIBNAME ${TIFF_LIBRARIES})
+   SET(TIFF_INCLUDE_DIRNAME ${TIFF_INCLUDE_DIR})
+ ENDIF(TIFF_FOUND)
+#
+ SET(LCMS12_MISSING 1)
+ INCLUDE(${OPENJPEG_SOURCE_DIR}/thirdparty/FindLCMS2.cmake OPTIONAL)
+#
+ IF(LCMS2_FOUND)
+  SET(LCMS12_MISSING 0)
+  SET(HAVE_LCMS2_H 1)
+  SET(HAVE_LIBLCMS2 1)
+  SET(LCMS_LIBNAME ${LCMS2_LIBRARY})
+  SET(LCMS_INCLUDE_DIRNAME ${LCMS2_INCLUDE_DIR})
+ ENDIF(LCMS2_FOUND)
+#
+ IF(NOT LCMS2_FOUND)
+  INCLUDE(${OPENJPEG_SOURCE_DIR}/thirdparty/FindLCMS.cmake OPTIONAL)
+#
+  IF(LCMS_FOUND)
+   SET(LCMS12_MISSING 0)
+   SET(HAVE_LCMS1_H 1)
+    SET(HAVE_LIBLCMS1 1)
+    SET(LCMS_LIBNAME ${LCMS_LIBRARY} )
+    SET(LCMS_INCLUDE_DIRNAME ${LCMS_INCLUDE_DIR})
+  ENDIF(LCMS_FOUND)
+ ENDIF(NOT LCMS2_FOUND)
+#-------------------------------------------------------------
+ OPTION(BUILD_THIRDPARTY "Build the thirdparty executables" ON)
+#
+ IF(NOT ZLIB_FOUND OR NOT PNG_FOUND OR NOT TIFF_FOUND OR LCMS12_MISSING) 
+  IF(BUILD_THIRDPARTY)
+   SET(HAVE_ZLIB_H 1)
+   SET(HAVE_LIBZ 1)
+   SET(HAVE_PNG_H 1)
+   SET(HAVE_LIBPNG 1)
+   SET(HAVE_TIFF_H 1)
+   SET(HAVE_LIBTIFF 1)
+   SET(HAVE_LCMS2_H 1)
+   SET(HAVE_LIBLCMS2 1)
+#
+   ADD_SUBDIRECTORY(${OPENJPEG_SOURCE_DIR}/thirdparty)
+#
+   LINK_DIRECTORIES(${CMAKE_BINARY_DIR}/thirdparty/lib)
+#
+   IF(NOT ZLIB_FOUND)
+    INCLUDE_DIRECTORIES(${OPENJPEG_SOURCE_DIR}/thirdparty/include)
+    SET(ZLIB_INCLUDE_DIRNAME ${OPENJPEG_SOURCE_DIR}/thirdparty/include)
+    SET(Z_LIBNAME z)
+    SET(ZLIB_FOUND 1)
+   ENDIF(NOT ZLIB_FOUND)
+#
+   IF(NOT PNG_FOUND)
+    SET(PNG_INCLUDE_DIRNAME ${OPENJPEG_SOURCE_DIR}/thirdparty/libpng)
+    SET(PNG_LIBNAME png)
+    SET(PNG_FOUND 1)
+   ENDIF(NOT PNG_FOUND)
+#
+   IF(NOT LCMS_FOUND AND NOT LCMS2_FOUND)
+    SET(LCMS_INCLUDE_DIRNAME ${OPENJPEG_SOURCE_DIR}/thirdparty/liblcms2/include)
+    SET(LCMS_LIBNAME lcms2)
+    SET(LCMS2_FOUND 1)
+   ENDIF(NOT LCMS_FOUND AND NOT LCMS2_FOUND)
+#
+   IF(NOT TIFF_FOUND)
+    SET(TIFF_INCLUDE_DIRNAME ${OPENJPEG_SOURCE_DIR}/thirdparty/libtiff)
+    SET(TIFF_LIBNAME tiff)
+    SET(TIFF_FOUND 1)
+   ENDIF(NOT TIFF_FOUND)
+#
+  ENDIF(BUILD_THIRDPARTY)
+ ENDIF(NOT ZLIB_FOUND OR NOT PNG_FOUND OR NOT TIFF_FOUND OR LCMS12_MISSING)
+#
+ENDIF(BUILD_CODEC OR BUILD_MJ2)
+#
+IF(BUILD_CODEC)
+ ADD_SUBDIRECTORY(codec)
+ENDIF(BUILD_CODEC)
+#
+IF(BUILD_MJ2)
+ ADD_SUBDIRECTORY(mj2)
+ENDIF(BUILD_MJ2)
+#
+IF(BUILD_INDEXER_JPIP)
+ ADD_SUBDIRECTORY(indexer_JPIP)
+ENDIF(BUILD_INDEXER_JPIP)
+#
\ No newline at end of file
diff --git a/applications/codec/CMakeLists.txt b/applications/codec/CMakeLists.txt
index 791d13b8..02d90fc5 100644
--- a/applications/codec/CMakeLists.txt
+++ b/applications/codec/CMakeLists.txt
@@ -4,14 +4,14 @@
 SET(common_SRCS
   convert.c
   index.c
-  ${OPENJPEG_SOURCE_DIR}/common/color.c
+  ${OPENJPEG_SOURCE_DIR}/applications/common/color.c
 )
 
 # If not getopt was found then add it to the lib:
 IF(DONT_HAVE_GETOPT)
   SET(common_SRCS
     ${common_SRCS}
-    ${OPENJPEG_SOURCE_DIR}/common/getopt.c
+    ${OPENJPEG_SOURCE_DIR}/applications/common/getopt.c
   )
 ENDIF(DONT_HAVE_GETOPT)
 
@@ -19,7 +19,7 @@ ENDIF(DONT_HAVE_GETOPT)
 INCLUDE_DIRECTORIES(
   ${OPENJPEG_SOURCE_DIR}/libopenjpeg
   ${LCMS_INCLUDE_DIRNAME}
-  ${OPENJPEG_SOURCE_DIR}/common
+  ${OPENJPEG_SOURCE_DIR}/applications/common
   ${Z_INCLUDE_DIRNAME}
   ${PNG_INCLUDE_DIRNAME}
   ${TIFF_INCLUDE_DIRNAME}
@@ -55,12 +55,42 @@ ENDFOREACH(exe)
 
 # Install man pages
 INSTALL(
-  FILES       ../doc/man/man1/image_to_j2k.1
-              ../doc/man/man1/j2k_dump.1
-              ../doc/man/man1/j2k_to_image.1
+  FILES       ${OPENJPEG_SOURCE_DIR}/doc/man/man1/image_to_j2k.1
+              ${OPENJPEG_SOURCE_DIR}/doc/man/man1/j2k_dump.1
+              ${OPENJPEG_SOURCE_DIR}/doc/man/man1/j2k_to_image.1
   DESTINATION ${OPENJPEG_INSTALL_MAN_DIR}/man1)
 #
 
+IF(BUILD_JPWL)
+  ADD_EXECUTABLE(JPWL_j2k_to_image
+  j2k_to_image.c
+  ${common_SRCS}
+  )
+
+  TARGET_LINK_LIBRARIES(JPWL_j2k_to_image ${OPENJPEG_LIBRARY_NAME}_JPWL
+    ${LCMS_LIBNAME} ${Z_LIBNAME} ${PNG_LIBNAME} ${TIFF_LIBNAME})
+  #
+  IF(UNIX)
+    TARGET_LINK_LIBRARIES(JPWL_j2k_to_image m)
+  ENDIF(UNIX)
+
+  ADD_EXECUTABLE(JPWL_image_to_j2k
+  image_to_j2k.c
+  ${common_SRCS}
+  )
+
+  TARGET_LINK_LIBRARIES(JPWL_image_to_j2k ${OPENJPEG_LIBRARY_NAME}_JPWL 
+  	${LCMS_LIBNAME} ${Z_LIBNAME} ${PNG_LIBNAME} ${TIFF_LIBNAME})
+  #
+  IF(UNIX)
+    TARGET_LINK_LIBRARIES(JPWL_image_to_j2k m)
+  ENDIF(UNIX)
+
+  INSTALL(TARGETS JPWL_image_to_j2k JPWL_j2k_to_image
+    DESTINATION ${OPENJPEG_INSTALL_BIN_DIR} COMPONENT Applications
+  )
+ENDIF(BUILD_JPWL)
+
 if(BUILD_TESTING)
 # Do testing here, once we know the examples are being built:
 FILE(GLOB_RECURSE OPENJPEG_DATA_IMAGES_GLOB
diff --git a/applications/codec/convert.c b/applications/codec/convert.c
index 98d54358..d9a45b9a 100644
--- a/applications/codec/convert.c
+++ b/applications/codec/convert.c
@@ -45,7 +45,7 @@
 #include <png.h>
 #endif /* HAVE_LIBPNG */
 
-#include "../libopenjpeg/openjpeg.h"
+#include "openjpeg.h"
 #include "convert.h"
 
 /*
diff --git a/applications/codec/j2k_dump.c b/applications/codec/j2k_dump.c
index 508dd65c..543a7d79 100644
--- a/applications/codec/j2k_dump.c
+++ b/applications/codec/j2k_dump.c
@@ -45,8 +45,8 @@
 
 #include "opj_config.h"
 #include "openjpeg.h"
-#include "../libopenjpeg/j2k.h"
-#include "../libopenjpeg/jp2.h"
+#include "j2k.h"
+#include "jp2.h"
 #include "getopt.h"
 #include "convert.h"
 #include "index.h"
diff --git a/applications/mj2/CMakeLists.txt b/applications/mj2/CMakeLists.txt
index 6fd63dde..7b365678 100644
--- a/applications/mj2/CMakeLists.txt
+++ b/applications/mj2/CMakeLists.txt
@@ -2,7 +2,7 @@
 
 SET(common_SRCS "")
 IF(DONT_HAVE_GETOPT)
-  SET(common_SRCS ${OPENJPEG_SOURCE_DIR}/common/getopt.c)
+  SET(common_SRCS ${OPENJPEG_SOURCE_DIR}/applications/common/getopt.c)
 ENDIF(DONT_HAVE_GETOPT)
 
 # While mj2 executables do not use the API correctly, we do not link with the library but rather compile the sources files.
@@ -36,7 +36,7 @@ ENDIF(WIN32)
 # Headers file are located here:
 INCLUDE_DIRECTORIES(
   ${OPENJPEG_SOURCE_DIR}/libopenjpeg
-  ${OPENJPEG_SOURCE_DIR}/common
+  ${OPENJPEG_SOURCE_DIR}/applications/common
   ${LCMS_INCLUDE_DIRNAME}
   )
 
@@ -58,7 +58,7 @@ ADD_EXECUTABLE(mj2_to_frames
     ${common_SRCS}
     ${OPJ_SRCS}
     ${MJ2_SRCS}
-    ${OPENJPEG_SOURCE_DIR}/common/color.c
+    ${OPENJPEG_SOURCE_DIR}/applications/common/color.c
     )
 IF(LCMS_FOUND OR LCMS2_FOUND)
   TARGET_LINK_LIBRARIES(mj2_to_frames ${LCMS_LIBNAME})
@@ -92,4 +92,4 @@ IF(UNIX)
 ENDIF(UNIX)
 
 INSTALL(TARGETS frames_to_mj2 mj2_to_frames extract_j2k_from_mj2 wrap_j2k_in_mj2
-	DESTINATION bin)
+	DESTINATION ${OPENJPEG_INSTALL_BIN_DIR})
diff --git a/applications/mj2/extract_j2k_from_mj2.c b/applications/mj2/extract_j2k_from_mj2.c
index 0872df1d..2d4cedbc 100644
--- a/applications/mj2/extract_j2k_from_mj2.c
+++ b/applications/mj2/extract_j2k_from_mj2.c
@@ -31,8 +31,8 @@
 #include <string.h>
 
 #include "openjpeg.h"
-#include "../libopenjpeg/j2k.h"
-#include "../libopenjpeg/jp2.h"
+#include "j2k.h"
+#include "jp2.h"
 #include "mj2.h"
 
 /* -------------------------------------------------------------------------- */
diff --git a/applications/mj2/frames_to_mj2.c b/applications/mj2/frames_to_mj2.c
index f6b77658..27744c0d 100644
--- a/applications/mj2/frames_to_mj2.c
+++ b/applications/mj2/frames_to_mj2.c
@@ -30,10 +30,10 @@
 #include <string.h>
 
 #include "openjpeg.h"
-#include "../libopenjpeg/j2k_lib.h"
-#include "../libopenjpeg/j2k.h"
-#include "../libopenjpeg/jp2.h"
-#include "../libopenjpeg/cio.h"
+#include "j2k_lib.h"
+#include "j2k.h"
+#include "jp2.h"
+#include "cio.h"
 #include "mj2.h"
 #include "mj2_convert.h"
 #include "getopt.h"
diff --git a/applications/mj2/meta_out.c b/applications/mj2/meta_out.c
index ff80b5e5..b6795045 100644
--- a/applications/mj2/meta_out.c
+++ b/applications/mj2/meta_out.c
@@ -14,7 +14,7 @@ can be bound by the Open JPEG open-source license and disclaimer, expressed else
 
 #include <windows.h> /* for time functions */
 
-#include "../libopenjpeg/opj_includes.h"
+#include "opj_includes.h"
 #include "mj2.h"
 
 #include <time.h>
diff --git a/applications/mj2/mj2.c b/applications/mj2/mj2.c
index 131eacea..51c6b1bf 100644
--- a/applications/mj2/mj2.c
+++ b/applications/mj2/mj2.c
@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  */
 
-#include "../libopenjpeg/opj_includes.h"
+#include "opj_includes.h"
 #include "mj2.h"
 
 /** @defgroup JP2 JP2 - JPEG-2000 file format reader/writer */
diff --git a/applications/mj2/mj2_convert.c b/applications/mj2/mj2_convert.c
index 3e6c1229..cc74b3ff 100644
--- a/applications/mj2/mj2_convert.c
+++ b/applications/mj2/mj2_convert.c
@@ -26,7 +26,7 @@
 * POSSIBILITY OF SUCH DAMAGE.
 */
 
-#include "../libopenjpeg/opj_includes.h"
+#include "opj_includes.h"
 #include "mj2.h"
 
 /*  -----------------------	      */
diff --git a/applications/mj2/mj2_to_frames.c b/applications/mj2/mj2_to_frames.c
index 156a101c..c5a41602 100644
--- a/applications/mj2/mj2_to_frames.c
+++ b/applications/mj2/mj2_to_frames.c
@@ -31,9 +31,9 @@
 
 #include "opj_config.h"
 #include "openjpeg.h"
-#include "../libopenjpeg/j2k_lib.h"
-#include "../libopenjpeg/j2k.h"
-#include "../libopenjpeg/jp2.h"
+#include "j2k_lib.h"
+#include "j2k.h"
+#include "jp2.h"
 #include "mj2.h"
 #include "mj2_convert.h"
 
diff --git a/applications/mj2/mj2_to_metadata.c b/applications/mj2/mj2_to_metadata.c
index 90be6202..ed2ce413 100644
--- a/applications/mj2/mj2_to_metadata.c
+++ b/applications/mj2/mj2_to_metadata.c
@@ -11,7 +11,7 @@ Except for copyright, inclusion of the code within Open JPEG for distribution an
 can be bound by the Open JPEG open-source license and disclaimer, expressed elsewhere.
 */
 
-#include "../libopenjpeg/opj_includes.h"
+#include "opj_includes.h"
 #include "mj2.h"
 
 #include "mj2_to_metadata.h"
diff --git a/applications/mj2/wrap_j2k_in_mj2.c b/applications/mj2/wrap_j2k_in_mj2.c
index 7766dd37..04ff7475 100644
--- a/applications/mj2/wrap_j2k_in_mj2.c
+++ b/applications/mj2/wrap_j2k_in_mj2.c
@@ -31,9 +31,9 @@
 #include <string.h>
 
 #include "openjpeg.h"
-#include "../libopenjpeg/j2k.h"
-#include "../libopenjpeg/jp2.h"
-#include "../libopenjpeg/cio.h"
+#include "j2k.h"
+#include "jp2.h"
+#include "cio.h"
 #include "mj2.h"
 
 static int int_ceildiv(int a, int b) {
diff --git a/libopenjpeg/CMakeLists.txt b/libopenjpeg/CMakeLists.txt
index 8cb6e295..8f6c9f98 100644
--- a/libopenjpeg/CMakeLists.txt
+++ b/libopenjpeg/CMakeLists.txt
@@ -1,24 +1,24 @@
 INCLUDE_REGULAR_EXPRESSION("^.*$")
 # Defines the source code for the library
 SET(OPENJPEG_SRCS
-  bio.c
-  cio.c
-  dwt.c
-  event.c
-  image.c
-  j2k.c
-  j2k_lib.c
-  jp2.c
-  jpt.c
-  mct.c
-  mqc.c
-  openjpeg.c
-  pi.c
-  raw.c
-  t1.c
-  t2.c
-  tcd.c
-  tgt.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/bio.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/cio.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/dwt.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/event.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/image.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/j2k.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/j2k_lib.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/jp2.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/jpt.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/mct.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/mqc.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/openjpeg.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/pi.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/raw.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/t1.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/t2.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/tcd.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/tgt.c
 )
 
 # Build the library
@@ -35,6 +35,11 @@ IF(UNIX)
 ENDIF(UNIX)
 SET_TARGET_PROPERTIES(${OPENJPEG_LIBRARY_NAME} PROPERTIES ${OPENJPEG_LIBRARY_PROPERTIES})
 
+# Build the JPWL library ?
+IF(BUILD_JPWL)
+ ADD_SUBDIRECTORY(jpwl)
+ENDIF(BUILD_JPWL)
+
 # Install library
 INSTALL(TARGETS ${OPENJPEG_LIBRARY_NAME}
   EXPORT OpenJPEGTargets
@@ -43,12 +48,12 @@ INSTALL(TARGETS ${OPENJPEG_LIBRARY_NAME}
 
 # Install includes files
 INSTALL(FILES openjpeg.h
-  DESTINATION ${OPENJPEG_INSTALL_INCLUDE_DIR}/${subdir} COMPONENT Headers
+  DESTINATION ${OPENJPEG_INSTALL_INCLUDE_DIR}/${OPENJPEG_INSTALL_SUBDIR} COMPONENT Headers
 )
 INSTALL(CODE
-  "EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E create_symlink ${subdir}/openjpeg.h \$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/${OPENJPEG_INSTALL_INCLUDE_DIR}/openjpeg.h)")
+  "EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E create_symlink ${OPENJPEG_INSTALL_SUBDIR}/openjpeg.h \$ENV{DESTDIR}\${CMAKE_INSTALL_PREFIX}/${OPENJPEG_INSTALL_INCLUDE_DIR}/openjpeg.h)")
 
 # install man page of the library
 INSTALL(
-  FILES       ../doc/man/man3/libopenjpeg.3
+  FILES       ${OPENJPEG_SOURCE_DIR}/doc/man/man3/libopenjpeg.3
   DESTINATION ${OPENJPEG_INSTALL_MAN_DIR}/man3)
diff --git a/libopenjpeg/jpwl/CMakeLists.txt b/libopenjpeg/jpwl/CMakeLists.txt
index 7dbb3d68..52411779 100755
--- a/libopenjpeg/jpwl/CMakeLists.txt
+++ b/libopenjpeg/jpwl/CMakeLists.txt
@@ -2,33 +2,11 @@
 
 ADD_DEFINITIONS(-DUSE_JPWL)
 
-SET(OPJ_SRCS
-../libopenjpeg/bio.c
-../libopenjpeg/cio.c
-../libopenjpeg/dwt.c
-../libopenjpeg/event.c
-../libopenjpeg/image.c
-../libopenjpeg/j2k.c
-../libopenjpeg/j2k_lib.c
-../libopenjpeg/jp2.c
-../libopenjpeg/jpt.c
-../libopenjpeg/mct.c
-../libopenjpeg/mqc.c
-../libopenjpeg/openjpeg.c
-../libopenjpeg/pi.c
-../libopenjpeg/raw.c
-../libopenjpeg/t1.c
-../libopenjpeg/t2.c
-../libopenjpeg/tcd.c
-../libopenjpeg/tgt.c
-)
 SET(JPWL_SRCS crc.c jpwl.c jpwl_lib.c rs.c)
 
-SET(common_SRCS "")
-# If not getopt was found then add it to the lib:
-IF(DONT_HAVE_GETOPT)
-  SET(common_SRCS ${OPENJPEG_SOURCE_DIR}/common/getopt.c)
-ENDIF(DONT_HAVE_GETOPT)
+INCLUDE_DIRECTORIES(
+  ${OPENJPEG_SOURCE_DIR}/libopenjpeg
+  )
 
 # Build the library
 IF(WIN32)
@@ -38,7 +16,7 @@ IF(WIN32)
     ADD_DEFINITIONS(-DOPJ_STATIC)
   ENDIF(BUILD_SHARED_LIBS)
 ENDIF(WIN32)
-ADD_LIBRARY(${OPENJPEG_LIBRARY_NAME}_JPWL ${JPWL_SRCS} ${OPJ_SRCS})
+ADD_LIBRARY(${OPENJPEG_LIBRARY_NAME}_JPWL ${JPWL_SRCS} ${OPENJPEG_SRCS})
 SET_TARGET_PROPERTIES(${OPENJPEG_LIBRARY_NAME}_JPWL 
   PROPERTIES ${OPENJPEG_LIBRARY_PROPERTIES})
 
@@ -46,48 +24,3 @@ SET_TARGET_PROPERTIES(${OPENJPEG_LIBRARY_NAME}_JPWL
 INSTALL(TARGETS ${OPENJPEG_LIBRARY_NAME}_JPWL
   DESTINATION ${OPENJPEG_INSTALL_LIB_DIR} COMPONENT Libraries
 )
-
-# Build executables
-
-INCLUDE_DIRECTORIES(
-  ${OPENJPEG_SOURCE_DIR}/libopenjpeg
-  ${OPENJPEG_SOURCE_DIR}/common
-  ${ZLIB_INCLUDE_DIRNAME}
-  ${LCMS_INCLUDE_DIRNAME}
-  ${PNG_INCLUDE_DIRNAME}
-  ${TIFF_INCLUDE_DIRNAME}
-  )
-
-ADD_EXECUTABLE(JPWL_j2k_to_image
-../codec/j2k_to_image.c
-../codec/convert.c
-../codec/index.c
-${OPENJPEG_SOURCE_DIR}/common/color.c
-${common_SRCS}
-)
-
-TARGET_LINK_LIBRARIES(JPWL_j2k_to_image ${OPENJPEG_LIBRARY_NAME}_JPWL
-  ${LCMS_LIBNAME} ${Z_LIBNAME} ${PNG_LIBNAME} ${TIFF_LIBNAME})
-#
-IF(UNIX)
-  TARGET_LINK_LIBRARIES(JPWL_j2k_to_image m)
-ENDIF(UNIX)
-
-
-ADD_EXECUTABLE(JPWL_image_to_j2k
-../codec/convert.c
-../codec/index.c
-../codec/image_to_j2k.c
-${common_SRCS}
-)
-
-TARGET_LINK_LIBRARIES(JPWL_image_to_j2k ${OPENJPEG_LIBRARY_NAME}_JPWL 
-	${LCMS_LIBNAME} ${Z_LIBNAME} ${PNG_LIBNAME} ${TIFF_LIBNAME})
-#
-IF(UNIX)
-  TARGET_LINK_LIBRARIES(JPWL_image_to_j2k m)
-ENDIF(UNIX)
-
-INSTALL(TARGETS JPWL_image_to_j2k JPWL_j2k_to_image
-  DESTINATION ${OPENJPEG_INSTALL_BIN_DIR} COMPONENT Binaries
-)
diff --git a/libopenjpeg/jpwl/jpwl.c b/libopenjpeg/jpwl/jpwl.c
index 42c88718..8a876683 100644
--- a/libopenjpeg/jpwl/jpwl.c
+++ b/libopenjpeg/jpwl/jpwl.c
@@ -29,7 +29,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  */
 
-#include "../libopenjpeg/opj_includes.h"
+#include "opj_includes.h"
 
 #ifdef USE_JPWL
 
diff --git a/libopenjpeg/jpwl/jpwl_lib.c b/libopenjpeg/jpwl/jpwl_lib.c
index ea53c935..048a7345 100644
--- a/libopenjpeg/jpwl/jpwl_lib.c
+++ b/libopenjpeg/jpwl/jpwl_lib.c
@@ -31,7 +31,7 @@
 
 #ifdef USE_JPWL
 
-#include "../libopenjpeg/opj_includes.h"
+#include "opj_includes.h"
 #include <limits.h>
 
 /** Minimum and maximum values for the double->pfp conversion */
diff --git a/libopenjpeg/opj_includes.h b/libopenjpeg/opj_includes.h
index 418ca6fc..53a0c4a7 100644
--- a/libopenjpeg/opj_includes.h
+++ b/libopenjpeg/opj_includes.h
@@ -129,7 +129,7 @@ static INLINE long lrintf(float f){
 
 /* JPWL>> */
 #ifdef USE_JPWL
-#include "../jpwl/jpwl.h"
+#include "./jpwl/jpwl.h"
 #endif /* USE_JPWL */
 /* <<JPWL */
 
diff --git a/CTestConfig.cmake b/testing/CTestConfig.cmake
similarity index 100%
rename from CTestConfig.cmake
rename to testing/CTestConfig.cmake
diff --git a/CMake/CTestCustom.cmake.in b/testing/CTestCustom.cmake.in
similarity index 100%
rename from CMake/CTestCustom.cmake.in
rename to testing/CTestCustom.cmake.in