The git 2.9 release came with an experimental diff algorithm --compaction-heuristic. I've set up git, and git gui to use this.
However I can't figure out how to configure gitk to use this option. I'm aware of the .gitk config file, but I can't figure out how configure diff options.
Setting diff.compactionHeuristic true in your git config should be picked up by gitk.
git config --global diff.compactionHeuristic true
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