1) .nib files are readonly by default in XCode 4, the user cannot view or edit them.
2) Binary encryption can be done perhaps adopting from iOS to osx: Executable encryption check anti piracy measure
3) Organization can be done via drag and drop of folders: Create your folder in the filesystem, then drag it to the resource folder in XCode. In the following dialog select create folder reference for any added folder. The folder should be blue. This folder is copied to your bundle with its contents.