In a good design, the OS is in its own directory with its settings, and each app is in its own directory with its settings.
Like .. Linux?
On Linux, i have yet to find any desktop application (thats not part of a distro) that installs in the ever-the-same, proper directory since its v1.0 release. At least most of the time it is /opt/* or /usr/bin/* or /bin/* .. its time Linux got some proper application-sandboxing too. I should not need to be root to install software, there should be a userspace level that can manages sandsboxes only. The Synaptec Package Manager (same for apt-get) software installer was way ahead of its time compared to other OS, but why is it overtaken?
Insights on this are welcome .. but keep the blind MS/*ux hate-love to yourself.