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For instance I want to enable the SmoothScroll plugin on my PC's but I'd rather it be turned off on the macbook, as the default touch-scrolling works good on the mac. I find that Chrome does a very good job of synchronizing everything including the "Enabled" setting of each plugin. But I'd rather that be left alone so it can be customized based on the computer.

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The only way I can think of is to stop syncing extensions so that if you disable it on your mac it won't get disabled on your PC.

You could also use an extension like Context to select when extensions are enabled or disabled, or try Extension automation

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