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During custom application upgrades, is there a configuration to limit what files or directories to update?

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I have a custom application that does incremental loads from an external resource. I maintain a file with the latest timestamps so that each run I can read the file and pull the new data. My struggle is with how do I perform application upgrades without rolling these files back to their initial value. Is there a configuration that can be set to ignore file types or directories during a custom application upgrade? Please advise.

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