In the *nix world, everything is pretty self contained within its own directory.
You must be talking about some crazy, bizarro *nix world, as the one in this world tends to split directories up by what the files are for, not by application.
For example,
Very infrequently, apps will install their entire directory structure into something like
Mmm, you didn't think the T-1000 in Season Two was good?
Granted, the T-1000 wasn't shown doing Terminator-like things in every episode...
Also, Cromartie and Cameron were T-888s... the upgraded version of the kind Arnold is in the movies.
All the simple programs have been written.