[CMake] Redirect output from add_custom_target()

[Micha Renner]

I would try

        add_custom_target( ${doc_target_name}
             DEPENDS ${generated_conf}
             COMMAND ${doxygen_exe} ${generated_conf} 2 > filename
             WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
             COMMENT "Generating documentation using Doxygen"
         )

Micha