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Sure. Just drag the file to the notes field, holding down the option key as you do so. Or, use Edit->Attach File... and make sure the Embed the file in the document option is selected. If you don't do it correctly, only a link will be stored (which will look fine on your Mac, but won't show up at all on the iPad). The embedded file will show up in the Attachments section of the editor in OmniFocus on iPad. It also works for OmniPlan and OmniGraphSketcher files.

There are some potential problems with this approach:
  • Attaching too many files (or files of too large a size) will slow down syncing
  • Opening the file on the iPad creates a new copy of it in the app in which you opened it, and it isn't currently possible to put it back into OmniFocus after making changes

You can use the handy Attachments List window in OmniFocus for Mac to verify that you've successfully embedded the file(s), and to help you find embedded files which are past their sell-by date and should be removed.