Please try replacing MITK/CMake/BundleUtilities.cmake with this version:

http://cmake.org/gitweb?p=cmake.git;a=blob_plain;f=Modules/BundleUtilities.cmake;hb=40792a1a15f1ee3c0582486aac9182f8eaa1b316

New Error

override: /Users/hal9000/MBI/mitkDiffusion_Installer/MITK-superbuild/MITK-build/bin/plugins/liborg_blueberry_osgi.dylib
found file: /liborg_blueberry_osgi.dylib
override result:
Error copying file "/Users/hal9000/MBI/mitkDiffusion_Installer/MITK-superbuild/MITK-build/bin/plugins/liborg_blueberry_osgi.dylib" to "/liborg_blueberry_osgi.dylib".

exe_dotapp_dir/='/Users/hal9000/MBI/mitkDiffusion_Installer/MBI-build/_CPack_Packages/Darwin/DragNDrop/MITK-Diffusion-1.0.0/MBIApp.app/'
item_substring=''
resolved_embedded_item='/liborg_blueberry_osgi.dylib'

Install or copy the item into the bundle before calling fixup_bundle.
Or maybe there's a typo or incorrect path in one of the args to fixup_bundle?

CMake Error at /Users/hal9000/MBI/mbiDI_release/MITK/CMake/BundleUtilities.cmake:568 (message):

cannot fixup an item that is not in the bundle...

Call Stack (most recent call first):

/Users/hal9000/MBI/mbiDI_release/MITK/CMake/BundleUtilities.cmake:656 (fixup_bundle_item)
/Users/hal9000/MBI/mitkDiffusion_Installer/MBI-build/Applications/MBIApp/cmake_install.cmake:748 (fixup_bundle)
/Users/hal9000/MBI/mitkDiffusion_Installer/MBI-build/Applications/cmake_install.cmake:35 (INCLUDE)
/Users/hal9000/MBI/mitkDiffusion_Installer/MBI-build/cmake_install.cmake:295 (INCLUDE)

CPack Error: Error when generating package: MITK-Diffusion
make: *** [package] Error 1
[~/MBI/mitkDiffusion_Installer/MBI-build]:

When building sanboxapp only, same errors occour

so far i figured out, blueberry based dylibs shall be copied into directory SandboxApp/Contents/MacOS/plugins of the SandboxApp. Other dylibs, like libmbilog.dylib, libCTKCore.0.1.dylib etc. are stored in SanboxApp/Contents/MacOS/ directory. these files do not call an error. One could assume that something with the /plugin path has to be adjusted.

here calling the protocol in the cmake file:

function(fixup_bundle_item resolved_embedded_item exepath dirs)
get_item_key("${resolved_embedded_item}" ikey)
...
...
...
____ikey: 'libPocoXML_1_3_5_dylib'
fixup_bundle_item("${$_RESOLVED_EMBEDDED_ITEM}" "${exepath}" "${dirs}")

file in path: SanboxApp/Contents/MacOS/ NO ERROR

____ikey: 'libmbilog_dylib'
fixup_bundle_item("${$_RESOLVED_EMBEDDED_ITEM}" "${exepath}" "${dirs}")

file in path: SanboxApp/Contents/MacOS/ NO ERROR

____ikey:'liborg_blueberry_osgi_dylib'
fixup_bundle_item("${$_RESOLVED_EMBEDDED_ITEM}" "${exepath}" "${dirs}")

file shall be in path: SanboxApp/Contents/MacOS/plugins ERROR

How can we fix this?

Additional debug output:

In CMake/mitkMacroInstall.cmake, line 42, please add:

MESSAGE(\"override before: \${item}\")

DI installer binary built.
for success several subprojets of mbi are comment-out.

SET(MITK_DEFAULT_SUBPROJECTS MBI-Modules)

2. The order of the entries in this file is not arbitrary. Modules depending
3. on other modules must be listed after their dependencies. #

#ADD_SUBDIRECTORY(PersistenceData)
ADD_SUBDIRECTORY(Registration)
ADD_SUBDIRECTORY(GEFileReader)
ADD_SUBDIRECTORY(GraphAlgorithms)
ADD_SUBDIRECTORY(VolumeMeshing)
ADD_SUBDIRECTORY(NavigationToolRegistration)
ADD_SUBDIRECTORY(Kinect)
ADD_SUBDIRECTORY(KinectUI)
ADD_SUBDIRECTORY(ToFProcessingMBI)
ADD_SUBDIRECTORY(ToFHardwareMBI)
ADD_SUBDIRECTORY(ToFUIMBI)
ADD_SUBDIRECTORY(CameraCalibration)
ADD_SUBDIRECTORY(DiffusionImaging)
ADD_SUBDIRECTORY(TargetingVisualization)

not compatible with VTK 5.6

ADD_SUBDIRECTORY(PathPlanning)
#ADD_SUBDIRECTORY(DICOM)
ADD_SUBDIRECTORY(StateMachines)
ADD_SUBDIRECTORY(Robopsy)
ADD_SUBDIRECTORY(daVinciTracking)
#ADD_SUBDIRECTORY(IGT)
ADD_SUBDIRECTORY(EndoTracking)
ADD_SUBDIRECTORY(NeedleNavigation)
ADD_SUBDIRECTORY(ExtendedMeshes)
ADD_SUBDIRECTORY(ShapeModel)
ADD_SUBDIRECTORY(LiverSegmentation)
ADD_SUBDIRECTORY(LiverLogicRapid)
ADD_SUBDIRECTORY(LiverUI)
ADD_SUBDIRECTORY(HDF5)
ADD_SUBDIRECTORY(IGTUI)
ADD_SUBDIRECTORY(LymphNodeTools)
ADD_SUBDIRECTORY(ShapeModelTools)
#ADD_SUBDIRECTORY(DicomIndexer)
#ADD_SUBDIRECTORY(QtDicomBrowser)
ADD_SUBDIRECTORY(AnisotropicRegistration)
ADD_SUBDIRECTORY(OpenCVPredictionFilter)
#ADD_SUBDIRECTORY(XDLFL)
#ADD_SUBDIRECTORY(FollowUpRegistration)
ADD_SUBDIRECTORY(PCAFiltering)
ADD_SUBDIRECTORY(USIntelligentNeedleFinding)
ADD_SUBDIRECTORY(AbdomenSegmentation)
ADD_SUBDIRECTORY(OpenCL)
ADD_SUBDIRECTORY(LegFinder)
ADD_SUBDIRECTORY(ParticleFilter)
ADD_SUBDIRECTORY(NaviBroncho)
ADD_SUBDIRECTORY(ItkAlgorithms)
#ADD_SUBDIRECTORY(VesselSegmentation)
#ADD_SUBDIRECTORY(VesselSegmentationUI)
#ADD_SUBDIRECTORY(FatSegmentation)
#ADD_SUBDIRECTORY(Mitral)
#ADD_SUBDIRECTORY(MitralUI)
ADD_SUBDIRECTORY(3DSurfaceInterpolation)
ADD_SUBDIRECTORY(IntensityNormalization)
ADD_SUBDIRECTORY(GroupStatistics)
ADD_SUBDIRECTORY(SurfaceReconstruction)
ADD_SUBDIRECTORY(LungPerfusionAnalysis)