Yes. Most apps were 'installed' as a self-contained directory beginning with a '!', wherever you wanted. Double-clicking on such a directory ran the '!Run' script within it, which started the app. You could open up the app to see its component files by holding shift while double-clicking.
It was really quite a lovely system (very few installer programs, install/uninstall very clean with minimal dependencies), but it managed as well as it did mainly because nearly everything was statically linked and did its own thing for config. So centralised management of preferences was difficult, and what shared code there was (like the C library) broke the model a bit by needing to be kept in a separate '!System' directory.
As systems got more complex and ended up on the Internet, there was a greater concern for shared state between applications and security. Consequently the amount of stuff that started from disc on startup, the number of shared libraries and config files etc. went up, and some of the advantages of booting from ROM and the minimal 'copy to install' model went away a bit.
