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I think you're referring to the state-based approach where the deployment is based on comparing the source state with the target state. If so, Flyway supports this approach. When you create a project in Flyway Desktop make sure you set the deployment source as "schema model", which means deployments are calculated at deployment time, and no flyway_schema_history is required.
(If you're not referring to the state-based approach, I'd be interested in hearing more!)
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flyway_schema_history
table, is pretty invasive. The source of truth for a schema definition can be the script itself (the latest version if there are multiple versions) and all that a user expects from Flyway is that to query the details of a schema and reconcile with the script, make the changes as needed.