Hi, thanks for the pull request. I agree that it makes sense to compile src/ply/ply_parser.cpp into the pcl_io target. However, I would not remove pcl_io_ply yet, since people might link to it (as recommended in the issue), and simply removing it would break their builds. Ideally, we would add some kind of deprecation warning to pcl_io_ply that is displayed when someone tries to use it (link to it), but I currently have no idea how we could do that.
So I would suggest the following: Keep pcl_io_ply unchanged for now, add src/ply/ply_parser.cpp to the sources of pcl_io, and also keep PCL_ADD_INCLUDES(...) (because otherwise, projects using PCL won't find those ply headers).