The best way to include an addon is to use projectGenerator, which is included in the recent release versions of oF (you can find it directly under the extracted folder. If not, download the latest oF).
Including addons manually is very tricky as you mentioned. The file hierarchy is just a list of files to compile, so Xcode will compile them but does not refer to the include files in the hierarchy. There are several ways to add include files, but the easiest way is to use projectGenerator (or, copying an example project is not the cleanest way, but often useful).
