There is no way to reliably bring up a modern system with an empty /usr, there are two alternatives to fix it: copy /usr back to the rootfs or use an initramfs which can hide the split-off from the system.
Historically /bin, /sbin, /lib had the purpose to contain the utilities to mount /usr. This role can now be taken by the initramfs. Because the initramfs knows, where to find the root partition (which includes /etc), it can parse /etc/fstab and other configuration files and mount /usr before it finally switches the root partition and executes /usr/bin/init. From this point on init mounts the remaining partitions in /etc/fstab and the system starts as usual.
The long-term plan is to clean up the mess and confusion the current split of / vs. /usr has created. All tools will move back to /usr where they belong, and the rootfs will only contain compat-symlinks into /usr. Almost the entire system installed by packages will reside in /usr. This will split all non-host specific data to /usr. /usr can then be seen as the Unix System Resources partition (/System), which defines the base operating system (e.g. F18 or RHEL-7).
This new /usr could be mounted read-only by default, while the rootfs is read-write and contains only empty mount points, compat-symlinks to /usr and the host-specific data like /etc, /root, /srv. Compared to today’s setups, the rootfs will be very small. The new /usr could also easily be shared read-only across several systems, and it would contain almost the entire system. Such setups are more efficient, can optionally provide a lot more security, are more flexible, provide more sane options for custom setups, and are much simpler to setup and maintain.
This leaves us with the following well-defined directories, which compose the base of the system:
- /usr – installed system; shareable; possibly read-only
- /etc – config data; non-shareable
- /var – persistent data; non-shareable;
- /run – volatile data; non-shareable; mandatory tmpfs filesystem
/ |-- etc |-- usr | |-- bin | |-- sbin | |-- lib | `-- lib64 |-- run |-- var |-- bin -> usr/bin |-- sbin -> usr/sbin |-- lib -> usr/lib `-- lib64 -> usr/lib64
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