No leave those files and folders be, the SDK compiles as a single project, none of the tools in the SDK are seperate plugins (you’d have to edit the main.cpp file to remove their registration calls as otherwise you’ll get errors about missing files if you just remove them). The result of the compile is a cinema4dsdk.dylib file in the Cinema4DSDK folder, that is the plugin. You do not need to do anything else.
You shouldn’t attempt to modify the project itself unless you know what you’re doing as otherwise you will most probably end up screwing up the project and stopping it form compiling correctly. It’s designed to compile from the off without any need to change anything (apart from the intermediate build paths in XCodes general preferences), you really shouldn’t attempt to do anything other than just compile the project given your current level of understanding as you’re just making your life a lot more difficult and complex than it needs to be (it really is very simple to compile provided you just follow the basic instructions, i.e. load project, set intermediate paths, build).
Now that you’ve been mesing a lot of things around you may find that you will need to delete all the SDK and intermediate build folders and reinstall them (possibly reinstalling C4D). Remember that the intermediate paths should not be in your plugin folder itself, but outside of the whole plugins folder somewhere (anywhere it’s jsut temporary files, but it also contains things like intermediate builds of the dylibs that will interfere with your main plugin loading in correctly).