class Merger extends AbstractMerger {

	public Merger() {
		setRegistry(EMFCompareRCPPlugin.getDefault().getMergerRegistry());
	}

	@Override
	public boolean isMergerFor(Diff target) {
		// TODO Auto-generated method stub
		return false;
	}

	@Override
	public void copyRightToLeft(Diff target, Monitor monitor) {
		this.mergeDiff(target, true, monitor);
	}

	@Override
	public void copyLeftToRight(Diff target, Monitor monitor) {
		this.mergeDiff(target, false, monitor);
	}
}

EObject left = ....;
EObject right = ....;

IComparisonScope scope = new DefaultComparisonScope(left, right, null);
EMFCompare build = EMFCompare.builder().build();
Comparison comparison = build.compare(scope);
List<Diff> differences = comparison.getDifferences();

Merger merger = new Merger();
BasicMonitor monitor = new BasicMonitor();
for (Diff diff : differences)
{
		// if reference, use the merger.
		merger.copyLeftToRight(diff, monitor);
		diff.setState(DifferenceState.UNRESOLVED);
	}
}

class Merger extends AbstractMerger {

	/**
	 * We want to bypass the reference merger that is eventually called by the 
	 * abstract merger, so we create this merger with a very high ranking.
	 * 
	 * The goal of the bypass is th replace the operation createCopy, so that
	 * objects are not created multiple times.
	 *
	 */
	public static class CustomReferenceMerger extends ReferenceChangeMerger {

		final EcoreUtil.Copier copier = new EMFCompareCopier();

		protected EObject createCopy(EObject referenceObject) {

			if (copier.containsKey(referenceObject))
				return copier.get(referenceObject);
			return copier.copy(referenceObject);
		}

		@Override
		public int getRanking() {
			return Integer.MAX_VALUE;
		}

	}

	public Merger() {
		setRegistry(EMFCompareRCPPlugin.getDefault().getMergerRegistry());
		getRegistry().add(new CustomReferenceMerger());
	}

	@Override
	public boolean isMergerFor(Diff target) {
		// TODO Auto-generated method stub
		return false;
	}

	@Override
	public void copyRightToLeft(Diff target, Monitor monitor) {
		this.mergeDiff(target, true, monitor);
	}

	@Override
	public void copyLeftToRight(Diff target, Monitor monitor) {
		this.mergeDiff(target, false, monitor);
	}

}