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By default, files larger than 4KB are stored on disk named after their SHA1 digest, in the directory fcrepo.binary.directory. (4KB is the default, but can be changed by updating thethe minimumBinarySizeInBytes property in repository.json).
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That is, a file with the SHA1 "a1b2c369563c0465ab82cdb2789d45ce1c3585b1" would be stored on disk in /path/to/fcrepo4-data/fcrepo.binary.directory/a1/b2/c3/a1b2c369563c0465ab82cdb2789d45ce1c3585b1. So files in the repository can be backed up backing up the directory fcrepo.binary.directory.