- disabled OPTIMIZE_OUTPUT_JAVA
- filtered out *.m scripts
- removed link to old Sphinx documentation
- replaced all mentions of Sphinx with Doxygen

- updated existing Doxyfile.in
- added corresponding cmake instructions
- added some specific files (layout, icon)
- clean existing doxygen warnings

Conflicts:
	CMakeLists.txt
	doc/CMakeLists.txt
	modules/core/include/opencv2/core.hpp
	modules/core/include/opencv2/core/base.hpp
	modules/core/include/opencv2/core/cuda.inl.hpp
	modules/core/include/opencv2/core/mat.hpp
	modules/core/include/opencv2/core/matx.hpp
	modules/core/include/opencv2/core/types.hpp
	modules/flann/include/opencv2/flann/lsh_table.h
	modules/imgproc/include/opencv2/imgproc.hpp

- updated existing Doxyfile.in
- added corresponding cmake instructions
- added some specific files (layout, icon)
- clean existing doxygen warnings