Currently, there are two separate 'Output' windows: in main window and 'Log'. I suggest to synchronize them, that is, make sure they have identical content at all times.
Depending on where you run a command from, its output ends up in one of those. I routinely run 'Rebase HEAD to...' from Log, then 'Continue rebase' from main window. Parts of the output ends up in 'Log', and another part in main window. To make matters worse, closing and reopening Log window during rebase will wipe its portion of 'Output'.
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