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I’ve tried installing and activating Jetpack on WordPress installations with Fuji theme activated and it seems to be working fine. In order for me to be able to troubleshoot the situation, could you please provide more details on the nature of the problem: what parts of the theme got messed up and how?
I’m having a lot of problems with Jetpack and Fuji. I decided to deactivate Jetpack for now till I have the theme ready. I’ll update you when I get Jetpack running again.