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If I click on an unstaged file multiple times the compare editor is not reused, and I get multiple compare editors opened.
An additional note: double clicking on staged changes does reuse the compare editor. So as the OP noted, it's just unstaged changes.
Proposed patch at; http://egit.eclipse.org/r/3859 This also changes the Compare With->HEAD Revision as they are using the same handler.
merged as 2cbdb149e64d00ce161f556220cf5aabb212e4e3