System layout

First, OSTree encourages systems to implement UsrMove. This is simply to avoid the need for more bind mounts. By default OSTree's dracut hook creates a read-only bind mount over /usr; you can of course generate individual bind-mounts for /bin, all the /lib variants, etc. So it is not intended to be a hard requirement.

Remember, because by default the system is booted into a chroot equivalent, there has to be some way to refer to the actual physical root filesystem. Therefore, your operating system tree should contain an empty /sysroot directory; at boot time, OSTree will make this a bind mount to the physical / root directory. There is precedent for this name in the initramfs context. You should furthermore make a toplevel symbolic link /ostree which points to /sysroot/ostree, so that the OSTree tool at runtime can consistently find the system data regardless of whether it's operating on a physical root or inside a deployment.

Because OSTree only preserves /var across upgrades (each deployment's chroot directory will be garbage collected eventually), you will need to choose how to handle other toplevel writable directories specified by the Filesystem Hierarchy Standard. Your operating system may of course choose not to support some of these such as /usr/local, but following is the recommended set:

Furthermore, since /var is empty by default, your operating system will need to dynamically create the targets of these at boot. A good way to do this is using systemd-tmpfiles, if your OS uses systemd. For example:

d /var/log/journal 0755 root root -
L /var/home - - - - ../sysroot/home
d /var/opt 0755 root root -
d /var/srv 0755 root root -
d /var/roothome 0700 root root -
d /var/usrlocal 0755 root root -
d /var/usrlocal/bin 0755 root root -
d /var/usrlocal/etc 0755 root root -
d /var/usrlocal/games 0755 root root -
d /var/usrlocal/include 0755 root root -
d /var/usrlocal/lib 0755 root root -
d /var/usrlocal/man 0755 root root -
d /var/usrlocal/sbin 0755 root root -
d /var/usrlocal/share 0755 root root -
d /var/usrlocal/src 0755 root root -
d /var/mnt 0755 root root -
d /run/media 0755 root root -

Particularly note here the double indirection of /home. By default, each deployment will share the global toplevel /home directory on the physical root filesystem. It is then up to higher levels of management tools to keep /etc/passwd or equivalent synchronized between operating systems.

Each deployment can easily be reconfigured to have its own home directory set simply by making /var/home a real directory.