I guess that /usr is probably on the same partition as his root.. But depending on the distro, and how the system is managed; it may be the case that every sing

I guess that /usr is probably on the same partition as his root.. But depending on the distro, and how the system is managed; it may be the case that every single file in /usr comes from a package, and can be cryptographically verified using your package manager (this is certainly possible with RedHat, Debian + derivatives at least). As long as /var or wherever your package DB lives is encrypted..