handling multiple partitions with codonPartitionedRobustCounting & dNdSLogger

[plemey]

In order to handle multiple partitions in renaissance counting, a prefix is added to codonPartitionedRobustCounting:

	<codonPartitionedRobustCounting id="PA.robustCounting1" labeling="S" prefix="PA." saveCompleteHistory="false" useUniformization="true" unconditionedPerBranch="true">
		<treeModel idref="treeModel"/>
		<firstPosition>
			<ancestralTreeLikelihood idref="PA.CP1.treeLikelihood"/>
		</firstPosition>
		<secondPosition>
			<ancestralTreeLikelihood idref="PA.CP2.treeLikelihood"/>
		</secondPosition>
		<thirdPosition>
			<ancestralTreeLikelihood idref="PA.CP3.treeLikelihood"/>
		</thirdPosition>
	</codonPartitionedRobustCounting>

But dNdSLogger was so fa expecting annotations without such a prefix. This can be fixed by adding the prefix also to dNdSLogger:
		<log id="fileLog_dNdS_PA" logEvery="1000" fileName="PA-HA-NA-MP_no_overlap.RC.base.PA.dNdS.log">
			<dNdSLogger id="PA.dNdS" prefix="PA.">
				<treeModel idref="treeModel"/>
				<codonPartitionedRobustCounting idref="PA.robustCounting1"/>
				<codonPartitionedRobustCounting idref="PA.robustCounting2"/>
			</dNdSLogger>
		</log

So, if beauti can also add the prefixes to the logger, this would solve the issue.