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If I used virtualbox to create a snapshot template of a preconfigured linux machine and wanted to ensure that no one has tampered with my snapshot, could I simply keep a comparable hash of the VDI file? This sounds overly simple, am I missing something?

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Excluding a hash collision (possible but unlikely/difficult) and someone altering your "secure" copy of the hash, I think you got it. You should, of course, run the hashes when the VM is shut down.

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