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I think ignoring whole system changes would be a bad thing, because it would imply undesirable behaviour to my POV (lots of commits are made by SYSTEM ... not keeping this changes would go against the backup feature of the plugin).
But your use case is interesting though. Maybe could I track some "causes" for SYSTEM modification and allow to disable syncing on certain "causes" (one of the cause would be the hack by the EnvInject plugin![]()
)