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It would be nice if the diff/compare would use color to explicitly illustrate what type of change has happened between the two files. Green for new code, Red for deleted code, blue for changed code could be a possibility. Programs like CVSweb and Araxis merge use this scheme already.
Yes, for the two way compare case we could use color coding to indicate the kind of change. However, in the three-way compare case we consider the direction of a change (incoming, outgoing, deletion) more important than the type of a change. Therefore we use color coding for the change direction: blue- incoming, black-outgoing, red-conflicting. As a consequence we don't use two different color codings for the two-way and the three-way compare case because that would confuse users even more...
Even if there is no color coding for incoming/outgoing or new/deleted code, the color of the changes should be configurable. On my system the compare color is almost identical to the text background color (this changed sometime between 20020321 and 2.0), so even if the color is not configurable yellow is a better choice.
after 2.1
reopening since workbench theme UI has become available
Workbench theme UI is used for specifying compare colors since M8.