> "the /usr split is there for a reason!". No, it's just an historical quirk.
It's a historical quirk on linux, where there is no clear separation between "base OS packages" and "3rd party packages".
On FreeBSD the split is very real, anything in /bin/ ships with my OS and is maintained and updated by the FreeBSD team. Anything in /usr/bin/ comes from ports and is thus a 3rd party package I installed and can be safely nuked and I need to maintain/update it.
> It's a historical quirk on linux, where there is no clear separation between "base OS packages" and "3rd party packages".
It was a historical quirk to start with. At Bell Labs, back in the early 1970s, Unix was being developed on PDP-11s with RK05 hard disks (with removable disk packs), which had an amazingly generous capacity of 2.5MB each. The Unix operating system had grown too big to fit on a single RK05 disk volume so they had to split it across two. Other operating systems of the period faced similar issues, but dealt with them in (arguably) more elegant ways – on IBM mainframes, OS/360 maintained a database ("catalog") mapping file paths (dataset names, to use the proper terminology) to volume names, so you could move a file to another disk without changing its path. True to Unix's penchant for simplicity, its authors decided instead to just split the OS into / and /usr. And the split survived long after they'd upgraded to more spacious disks.
Any other explanation for the split is essentially a retcon. Some of those retcons (even if, as other commenters have pointed out, not your own) may actually have become true – some of them may have been approximately true to begin with, and they influenced people's decisions, thereby making themselves more true over time. But its ultimate origins will forever remain this quirk of computing history.
Funny aside: yours is an excellent comment, and yet proof that you didn't read the article, as the first part is almost word-for-word identical to the post.
I don't mean to shame you, I sometimes comment without reading TFA, and in your case you add a few more details that were not present in the article. I just found it interesting.
A much better separation is achieved in a few Linux distributions where every package is installed in a separate directory.
All the files that might be expected by others to be in certain standard locations are sym-linked to those locations, e.g. the executables to /usr/bin,/usr/sbin,/bin or /sbin, in order to appear in PATH.
In this case you no longer need any kind of database to know which files may be safely nuked to delete any package.
Moreover, in FreeBSD there is no such separation between the "base OS packages" and "3rd party packages", implemented as a difference between root and /usr. You might have misremembered /usr/local, which is indeed a place for "3rd party packages" in all UNIX-derived operating systems.
There are many "base OS packages" that are installed in /usr/bin or in /usr/sbin.
In any FreeBSD system, you can see their source files in /usr/src/usr.bin and in /usr/src/usr.sbin.
I have been using FreeBSD for a quarter of century, since FreeBSD 2.0, and there has never been such a separation between root and /usr.
The separation between /bin and /usr/bin and the other similar pairs was made only to allow /usr to be unmounted, when it is on another device than the root device, but still have in the root file system the minimal set of tools needed for diagnosing and repairing any broken file system or network connection.
In ancient FreeBSD installations it was always recommended to have a separate small root partition, e.g. of a few hundred megabytes, and some large partitions for usr and var.
This original use has become completely obsolete, because now, for diagnosing and repairing problems, it is preferable to boot from an USB stick or from the network (using a ramdisk as root file system), and then run diagnostics or repair programs without touching even the root file system unless modifying it is intentional.
In FreBSD it might still be possible to put /usr on a different partition or device and then unmount /usr, but in many Linux distributions this traditional usage is broken, because some of the programs installed in the root directories need components installed in /usr, so when /usr is unmounted they stop working.
The split is even stronger on NetBSD, where /usr is the base OS and /usr/pkg what's installed by the user through pkgin (binary packages) or pkgsrc (ports).
Likewise, the system configuration goes to /etc while the userland configuration goes to /usr/pkg/etc.
All it takes to factory reset a NetBSD system is an rm -Rf /usr/pkg.
It's a historical quirk on linux, where there is no clear separation between "base OS packages" and "3rd party packages".
On FreeBSD the split is very real, anything in /bin/ ships with my OS and is maintained and updated by the FreeBSD team. Anything in /usr/bin/ comes from ports and is thus a 3rd party package I installed and can be safely nuked and I need to maintain/update it.