updating makefile to not clean built manual and doxygen doc when running clean-all
updating makefile to not clean built manual and doxygen doc when running clean-all

stan-dev/math,stan-dev/math,stan-dev/math,stan-dev/stan,stan-dev/math,stan-dev/math,stan-dev/stan,stan-dev/math,stan-dev/math,stan-dev/math,stan-dev/stan,stan-dev/stan,stan-dev/math,stan-dev/stan