I'm surprised that you've got this problem when FTPing programs; my experience has been that ftp usually starts up in ASCII mode (and I usually forget to put it into binary mode, resulting in me downloading a corrupted binary, smacking my head against the monitor, turning binary mode on, and repeating the download). I have seen it when Windows and *ix boxen are networked together; apparently some networking systems are bright enough to manage big-endian - little-endian conversions but not quite intelligent enough to do end-of-line correction.
Ovid's solution is clever. Hacking ftpd may be a "superior" solution, but Ovid would be doing this on somebody else's nickel, and those somebodies may not want to pay for it.
At that time  the chief engineer was almost always the chief test pilot as well. That had the fortunate result of eliminating poor engineering early in aviation.
—Igor Sikorsky, reported in AOPA Pilot
magazine February 2003.
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