Earlier quoted context omitted.
> Seriously though, rsync is your friend. :-) Even rsync might not be atomic enough for some situations[1] since it'll update files as it goes rather than in one huge transaction at the end. [1] I worked on the World Cup 2006 site for Yahoo! and we had this issue - solved with 'rsync --link-dest' and swapping symlinks.
Write a script. 1. stop service 2. copy files 3. start service
Hot patching wins, but needs good design to work in the first place.