Well for your example: Tag it with your project and maybe their purpose. I would have bought this more if you were talking about code, but even then an IDE cou

Well for your example: Tag it with your project and maybe their purpose. I would have bought this more if you were talking about code, but even then an IDE could simply make the project a single file (like OS X '.apps's) to contain the whole project. This is actually similar to how Xcode works where how you organize your project doesn't always relate to how it is on disk.