Honest question: why does it matter if it's one file or not? For example if you're deploying to a web server, it doesn't seem a big deal if you're uploading one file or several... so why the issue?
Apple's ".app" distribution format works just like that, while allowing the developer to have a directory structure for their convenience. App stores solve the problem in other ways, but there is no good app store for the web.
Also as soon as you have more than one file you can run into path issues.