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If I remember things right, 'refresh' was indeed like re-opening the repo and I had put it there in case the repo was modified some other way while this program was running. I agree that it'd be better if it didn't reset the navigation when it didn't need to.
(Thanks for reporting this and the other ideas. Unfortunately, I won't be able to work on them anytime soon...)
I was navigating the "Work Tree" and pressing refresh as the effect of resetting where I was in my navigation.
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