As I said, what's wrong is that organizing files in this way is that it necessitates something like a package manager to keep track of which files are associated with which applications. This is not a "nice" way to organize things, it's a needlessly complicated one as evidenced by the operating systems, both current and historical, that don't do that and don't need a package manager.

> Windows, for comparison, is hell, since applications install files pretty much where they want, and that's why Windows, in the long term, gets more polluted than Linux (worst offender - leftover DLL, which impact the system).

Applications rarely install files (other than configuration files) outside of their own 'Program Files' directory. What you are saying was true until about XP, IIRC, but generally isn't today.

In my opinion RiscOS, NeXT, the original MacOS and current MacOS have the right idea with their single-object applications. It prevents reuse, yes, but the majority of "shared" libraries are used by exactly one application anyway, and the continued interest in container technology are evidence of all the problems caused by trying to share everything anyway.