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Merges are never quite coming out right with diff. It's not really diff's fault. It just doesn't know about source code. It would be very interesting if the JDT had a source-code diff which could ignore non-structural differences, understand where method and class boundaries are and use that information to perform a better merge. -- Configuration Details -- Product: Eclipse 4.6.3.20170314-1500 (org.eclipse.epp.package.java.product)Installed Features: org.eclipse.jdt 3.12.3.v20170301-0400 Versioning Plugin: org.eclipse.platform 4.6.3.v20170301-0400