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What do you mean "protect hashes"? You calculate them. Your

program reads files and checks. They are not stored on your machine.
And of course people should be careful and not trust everyone. Not just in a context of rootkits or even computing in general.

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they exactly are stored in machine, for example arch, pacman on installation calculates hash of the package compressed file and compares with a hash from mirror and if it's ok so package will be installed and hashes of its files will be stored in mtree files on disk, -rw------- root:root. even rkhunter has some databases which contains known to be original hashes and compares with them. they all comes with packages and are stored in machine

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