Actually, the root account is locked on FW 5.3.x, so I have no idea if setting a password via passwd helps or not, but it does work pretty well with shared keys auth.
On one hand, you shouldn't need to use Kubrick just to change the root passwd, just use the passwd tool over usb, and tell us if it shouts at you because of the locked account
.
On the other hand, if it fails, and you don't want to use shared keys, then, yeah, maybe Kubrick resets the shadow/passwd files as part of some of the process, can't say, you'd have to ask people more familiar with Kubrick
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