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If you have system-wide backups running the infinite number of backup files created by OmniFocus can be a little annoying. Here's how to disable them:
  1. In Preferences, uncheck the "Also back up when quitting" option
  2. Quit OmniFocus
  3. Launch Terminal
  4. Enter defaults write com.omnigroup.OmniFocus AutomaticBackupMinutes -int 525600000
Backups will now occur once a millennia.

You can also set the backup path to /tmp:

defaults write com.omnigroup.OmniFocus AutomaticBackupFolder /tmp

Files written to /tmp will eventually be deleted by the system so if OmniFocus does create backups for some reason you won't have to do anything to get rid of them.