diff --git a/CMake/mitkSetupVariables.cmake b/CMake/mitkSetupVariables.cmake
index a47d6d097b..25a9a3e5aa 100644
--- a/CMake/mitkSetupVariables.cmake
+++ b/CMake/mitkSetupVariables.cmake
@@ -1,161 +1,161 @@
 if(MITK_BUILD_ALL_PLUGINS)
   set(MITK_BUILD_ALL_PLUGINS_OPTION "FORCE_BUILD_ALL")
 endif()
 
 set(LIBPOSTFIX "")
 
 # MITK_VERSION
 set(MITK_VERSION_MAJOR "2012")
 set(MITK_VERSION_MINOR "02")
 set(MITK_VERSION_PATCH "99")
 set(MITK_VERSION_STRING "${MITK_VERSION_MAJOR}.${MITK_VERSION_MINOR}.${MITK_VERSION_PATCH}")
 if(MITK_VERSION_PATCH STREQUAL "99")
   set(MITK_VERSION_STRING "${MITK_VERSION_STRING}-${MITK_REVISION_SHORTID}")
 endif()
 
 #-----------------------------------
 # Configuration of module system
 #-----------------------------------
 set(MODULES_CONF_DIRNAME modulesConf)
 set(MODULES_CONF_DIRS ${MITK_BINARY_DIR}/${MODULES_CONF_DIRNAME})
 
 if(NOT UNIX AND NOT MINGW)
   set(MITK_WIN32_FORCE_STATIC "STATIC" CACHE INTERNAL "Use this variable to always build static libraries on non-unix platforms")
 endif()
 
 # build the MITK_INCLUDE_DIRS variable
-set(MITK_INCLUDE_DIRS ${PROJECT_BINARY_DIR})
+set(MITK_INCLUDE_DIRS
+    ${ITK_INCLUDE_DIRS}
+    ${VTK_INCLUDE_DIRS}
+    ${PROJECT_BINARY_DIR} # contains mitkConfig.h and similar files
+    ${MODULES_CONF_DIRS} # contains module *Exports.h files
+   )
 set(CORE_DIRECTORIES Common DataManagement Algorithms IO Rendering Interactions Controllers Service)
 foreach(d ${CORE_DIRECTORIES})
   list(APPEND MITK_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/Core/Code/${d})
 endforeach()
 #list(APPEND MITK_INCLUDE_DIRS  
      #${ITK_INCLUDE_DIRS}
      #${VTK_INCLUDE_DIRS}
 #    )
      
 #foreach(d Utilities Utilities/ipPic Utilities/IIL4MITK Utilities/pic2vtk Utilities/tinyxml Utilities/mbilog)
 foreach(d Utilities Utilities/ipPic Utilities/pic2vtk Utilities/tinyxml Utilities/mbilog)
   list(APPEND MITK_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/${d})
 endforeach()
 list(APPEND MITK_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/Utilities/mbilog)
 
 if(WIN32)
   list(APPEND MITK_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ipPic/win32)
 endif()
 
 # additional include dirs variables
 set(ANN_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ann/include)
 set(IPSEGMENTATION_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ipSegmentation)
 
 # variables containing librariy names
 set(MITK_CORE_LIBRARIES Mitk)
 set(VTK_FOR_MITK_LIBRARIES
     vtkGraphics
     vtkCommon
     vtkFiltering
     vtkftgl
     vtkGraphics
     vtkHybrid
     vtkImaging
     vtkIO
     vtkParallel
     vtkRendering
     vtkVolumeRendering
     vtkWidgets
     ${VTK_JPEG_LIBRARIES}
     ${VTK_PNG_LIBRARIES}
     ${VTK_ZLIB_LIBRARIES}
     ${VTK_EXPAT_LIBRARIES}
     ${VTK_FREETYPE_LIBRARIES}
    )
 # TODO: maybe solve this with lib depends mechanism of CMake
 set(UTIL_FOR_MITK_LIBRARIES mitkIpPic mitkIpFunc mbilog)
 set(LIBRARIES_FOR_MITK_CORE
     ${UTIL_FOR_MITK_LIBRARIES}
     ${VTK_FOR_MITK_LIBRARIES}
     ${ITK_LIBRARIES}
    )
 set(MITK_LIBRARIES
     ${MITK_CORE_LIBRARIES}
     ${LIBRARIES_FOR_MITK_CORE}
     pic2vtk
     #IIL4MITK
     ipSegmentation
     ann 
    )
    
 # variables used in CMake macros which are called from external projects
 set(MITK_VTK_LIBRARY_DIRS ${VTK_LIBRARY_DIRS})
 set(MITK_ITK_LIBRARY_DIRS ${ITK_LIBRARY_DIRS})
 
 # variables containing link directories
 set(MITK_LIBRARY_DIRS ${CMAKE_LIBRARY_OUTPUT_DIRECTORY})                                                                                                              
 set(MITK_LINK_DIRECTORIES
     ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
     ${ITK_LIBRARY_DIRS}
     ${VTK_LIBRARY_DIRS}
     ${GDCM_LIBRARY_DIRS})
 
 # Qt support
 if(MITK_USE_QT)
   find_package(Qt4 REQUIRED)
 
   set(QMITK_INCLUDE_DIRS 
       ${MITK_INCLUDE_DIRS}
-      ${CMAKE_CURRENT_SOURCE_DIR}/CoreUI/Qmitk
-      ${PROJECT_BINARY_DIR}/CoreUI/Qmitk
+      ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Qmitk
+      ${PROJECT_BINARY_DIR}/Modules/Qmitk
      )
-     
-  foreach(d QmitkApplicationBase QmitkModels QmitkPropertyObservers) 
-    list(APPEND QMITK_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/CoreUI/Qmitk/${d})
-  endforeach()
-  list(APPEND QMITK_INCLUDE_DIRS ${QWT_INCLUDE_DIR})
   
-  set(QMITK_LIBRARIES Qmitk ${MITK_LIBRARIES} ${QT_LIBRARIES})
-  set(QMITK_LINK_DIRECTORIES ${MITK_LINK_DIRECTORIES} ${QT_LIBRARY_DIR})
+  set(QMITK_LIBRARIES Qmitk ${MITK_LIBRARIES})
+  set(QMITK_LINK_DIRECTORIES ${MITK_LINK_DIRECTORIES})
 endif()
 
 if(MITK_BUILD_ALL_PLUGINS)
   set(MITK_BUILD_ALL_PLUGINS_OPTION "FORCE_BUILD_ALL")
 endif()
 
 # create a list of types for template instantiations of itk image access functions
 function(_create_type_seq TYPES seq_var seqdim_var)
   set(_seq )
   set(_seq_dim )
   string(REPLACE "," ";" _pixeltypes "${TYPES}")
   foreach(_pixeltype ${_pixeltypes})
     set(_seq "${_seq}(${_pixeltype})")
     set(_seq_dim "${_seq_dim}((${_pixeltype},dim))")
   endforeach()
   set(${seq_var} "${_seq}" PARENT_SCOPE)
   set(${seqdim_var} "${_seq_dim}" PARENT_SCOPE)
 endfunction()
 
 set(MITK_ACCESSBYITK_PIXEL_TYPES )
 set(MITK_ACCESSBYITK_PIXEL_TYPES_SEQ )
 set(MITK_ACCESSBYITK_TYPES_DIMN_SEQ )
 foreach(_type INTEGRAL FLOATING COMPOSITE)
   set(_typelist "${MITK_ACCESSBYITK_${_type}_PIXEL_TYPES}")
   if(_typelist)
     if(MITK_ACCESSBYITK_PIXEL_TYPES)
       set(MITK_ACCESSBYITK_PIXEL_TYPES "${MITK_ACCESSBYITK_PIXEL_TYPES},${_typelist}")
     else()
       set(MITK_ACCESSBYITK_PIXEL_TYPES "${_typelist}")
     endif()
   endif()
 
   _create_type_seq("${_typelist}"
                    MITK_ACCESSBYITK_${_type}_PIXEL_TYPES_SEQ
                    MITK_ACCESSBYITK_${_type}_TYPES_DIMN_SEQ)
   set(MITK_ACCESSBYITK_PIXEL_TYPES_SEQ "${MITK_ACCESSBYITK_PIXEL_TYPES_SEQ}${MITK_ACCESSBYITK_${_type}_PIXEL_TYPES_SEQ}")
   set(MITK_ACCESSBYITK_TYPES_DIMN_SEQ "${MITK_ACCESSBYITK_TYPES_DIMN_SEQ}${MITK_ACCESSBYITK_${_type}_TYPES_DIMN_SEQ}")
 endforeach()
 
 set(MITK_ACCESSBYITK_DIMENSIONS_SEQ )
 string(REPLACE "," ";" _dimensions "${MITK_ACCESSBYITK_DIMENSIONS}")
 foreach(_dimension ${_dimensions})
   set(MITK_ACCESSBYITK_DIMENSIONS_SEQ "${MITK_ACCESSBYITK_DIMENSIONS_SEQ}(${_dimension})")
 endforeach()