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This can happen when you type RET on a hunk to visit the respective
file at the respective position. One solution to this problem is to
use global-reveal-mode. It makes sure that text around point is
always visible. If that is too drastic for your taste, then you may
instead use magit-diff-visit-file-hook to reveal the text, possibly
using reveal-post-command or for Org buffers org-reveal.