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Yes, you can create a folder that will not be crawled by the indexer. I haven't taken the time to test this, so I'm only offering broad strokes. In the [FeatureSettings] section of the config file, you can have a line like:
ExcludeSyncFolders=(\\.(?!kobo|adobe).+|([^.][^/]*/)+\\..+)
This is used by Nickel Menu to prevent the files from that installation to get added to the library. My Regular Expressions is a little rusty, but I think that already excludes any folder that starts with a . (other than .kobo or .adobe)
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