Calculate md5 on upload, and create file on server with md5 digest
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Assume a user is uploading 1234.dat to an FTP server, and is concerned that the file will make it across.
A really useful option for the integrity conscious out there would be for filezilla to calculate the md5sum of a file being uploaded (virtually free, since the entire file is being read anyway), and when the file transfer is complete, upload a file called 1234.dat.md5 (or perhaps md5/1234.dat) that contains the md5sum of the original file, so that it can be verified on the server side.
TCP handles integrity to some extent, but it is not the most robust method. Bugs in an FTP server could also be detected like this, and memory/disk errors on the FTP server.