Hi,
while generating my external mitk based application I had problems to let BLUEBERRY_USE_QT_HELP stay on while using a doxygen executable that is placed in a different folder compared to the mitk build.

In BlueBerryConfig.cmake generated by BlueBerry/BlueBerryConfig.cmake.in the cmake variable DOXYGEN_EXECUTABLE is overwritten in case it was defined before.

set(DOXYGEN_EXECUTABLE "@DOXYGEN_EXECUTABLE@"
or generated:
set(DOXYGEN_EXECUTABLE "C:/Programs/doxygen_1.8.7/doxygen.exe")

External projects that define the variable DOXYGEN_EXECUTABLE before calling find_package(mitk) in order to set it to a different location or even version should be allowed to do that.

BlueBerryConfig.cmake.in should be changed to call (ln 16):

set(DOXYGEN_EXECUTABLE "@DOXYGEN_EXECUTABLE@" CACHE FILEPATH "Doxygen executable")

to make it possible to define the variable first and then not to overwriting it.

I will create a branch in my Github fork in case it is interesting for others.