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In Protect, when a Alert Auto-Resolves or just Resolves, what does that mean. Did a file get quarantined? Is the file/program blocked but still on the device? Did it get deleted? Do we know?

Yes, the file gets quarantined inside this directory:

Library/Application Support/JamfProtect/Quarantine/<EVENT_UUID>


and also, the permissions are modified to strip off the execute permissions off the item before it gets moved to the quarantine 


Thank you!