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Commonly done by calculating and storing hash function digests of files to detect if two files with different names, edit dates, etc., have identical contents. Programs which do not support it, will behave as if the originally-named file/directory has been deleted and the newly named file/directory is new and transmit the "new" file again.
This file set has metadata including the file name, time stamps, attributes, address of first cluster location of the data, file lengths, and the file name. A checksum is taken over the entire file set, and a mismatch would occur if the directory file set was accidentally or maliciously changed.