LuaVoxelManip: Fix minor bug with set_lighting, remove coordinate params for light and liquid updates

On the lua side, notably minetest.env:<function>(<args>) should now
be replaced by minetest.<function>(<args>).
The old way is and will stay supported for a long time.

Also:
Update and clean up lua_api.txt (by celeron55)
Move EnvRef to lua and remove add_rat and add_firefly (by kahrl)
Add separate src/util/CMakeLists.txt, other minor fixes (by kahrl)

Remerge some files in order to reduce number of additional files

Make necessary changes for split, rename files, reorganize some bits