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There isn't a specific ignore option - and locations will scan recursively.
You might be able to craft a suitable list of locations using some of the wildcards supported in locations: https://documentation.red-gate.com/fd/Flyway-Locations-Setting-277579008.html
Otherwise, modifying the folder structure will likely be the best option
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Hello,
Is there an option for skipping subfolders under the path of the -locations flag ?
Thank you,
Ben