You just need to align your LOCATION clause of EXTERNALS TABLE's DDL to point to your /FLIGHT folder. Hive will crawl all the subfolders. You might also consider using PARTITION BY and instead of having folders for year, month a day. This let's you do things like WHERE my_partition_col > '19991115' AND my_partition_col < '20010215' which would be much tougher if you partition by specific year, month, and day values.
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