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Before we shipped, Tim spent some time improving the performance of the script you sent in OG #948637 and by the end of his tuning (in r194894) he had it running several times faster in OmniGraffle 6 than it was in OmniGraffle 5:
OG 5: 61s
OG 6: 14s
If you're seeing slow performance with some other use cases, we might need more data so we can tune those as well. (We saw some other opportunities for improving performance over the last few days, but didn't want to risk destabilizing the app as we approached the 6.0 release.)