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Do you run the sneaky peek builds? If you're running the production images, it seems like it shouldn't be too much of a headache, as the file in the latest build is identical to the one shipped in OmniFocus 1.0.1, and new production images don't come out all that often. Even if you do run the sneaky peeks, which would require reinstalling your changes more frequently, you probably could automate the process. Another approach would be to simply strip off the fixed Omni header and apply your own during your workflow processing....