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SmartGit uses the native controls. Those of Gnome 3 are excessively large. Please try using a different desktop.

It's the first menu item in the left most menu of the Conflict Solver. Where did you search?

No, this checkbox should be shown on each repository where you are pulling the first time - until you select it.

Can also perfectly be done from the Journal.

Just for my understanding: you have multiple remotes and in each one is a master you have checked out?