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Preferences > Team > Git: The first choice in the "Merge tool content" combo is "Ask the user when the tool is started". The UI should address the user directly, so use you/me, not "the user". Best solution in this case is to just say "Ask when the tool is started".
Proposed fix pushed to: http://egit.eclipse.org/r/4552 Updated to be "Prompt when starting tool"
merged as daa9d3da919189081e7f5b63f3461a036e51d424