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This may be in secondary literature #91 or it may belong as part of the specification, but either way, we should capture more guidance for repository operators (and repository tooling implementers).
Specifically for this issue, what should a repository do to recover from compromise?
For fast forward attacks, the Mercury paper makes some suggestions in section 5.3 and there's some more thoughts in https://github.com/theupdateframework/specification/pull/150/files#r710834950 and #150 more generally.