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When in the diff/changes view, it should be possible to have independent scrolling between the views.
Currently it's impossible to compare changes since one of the views might completely off. That might admittedly be another bug, but there is no fool-proof algorithm for determining which part of each view correspond to each other, so letting the user decide by allowing him to manually scroll would help a lot.
A nicer solution is to do what xcode 4 does.
When you scroll the scrollbar, the two sides move together. However, if one has a larger hunk, it alone moves until it's caught up with the other side.
Admittedly, it doesn't handle vertical moves like you mention, but on the whole it's a lot nice than our current solution. For than, an option to scroll independently *might* be useful, maybe a "link views" checkbox that could be unchecked.