replace FastRelaxedClockLogNormal to ORC

[walterxie]

For relaxed clock, replace FastRelaxedClockLogNormal to ORC https://github.com/jordandouglas/ORC/

https://doi.org/10.1371/journal.pcbi.1008322

[walterxie]

Tips:

1. LogNormal distr in prior can be reused in branchRateModel.
2. mean in real space has to be 1, otherwise there is scaling issue in MCMC. So, the lphy code must have branchRate LogNormal(mean in real=1, ...);.

<prior id="ORCRatePriorDistribution.c:CRC01" name="distribution" x="@ORCRates.c:CRC01">
                    <LogNormal id="LogNormalDistributionModel.0" S="@ORCsigma.c:CRC01" meanInRealSpace="true" name="distr">
                        <parameter id="RealParameter.47" spec="parameter.RealParameter" estimate="false" name="M">1.0</parameter>
                    </LogNormal>
                </prior>

<branchRateModel id="OptimisedRelaxedClock.c:CRC01" spec="beast.base.evolution.branchratemodel.UCRelaxedClockModel" clock.rate="@ORCucldMean.c:CRC01" rates="@ORCRates.c:CRC01" tree="@Tree.t:CRC01">
                        <LogNormal id="ORCLogNormalDistributionModel.c:CRC01" S="@ORCsigma.c:CRC01" meanInRealSpace="true" name="distr">
                            <parameter id="RealParameter.46" spec="parameter.RealParameter" estimate="false" name="M">1.0</parameter>
                        </LogNormal>
                    </branchRateModel>

[walterxie]

The incomplete dev is in branch b2.7ops https://github.com/LinguaPhylo/LPhyBeast/tree/b2.7ops

[walterxie]

use UCLN LinguaPhylo/linguaPhylo#488

[walterxie]

TODO: how to disable <operator id="YuleModelNarrow" spec="Exchange" tree="@Tree" weight="..."/>, which is duplicated between added extra operator and default tree operators?

LPhyBeast/lphybeast/src/main/java/lphybeast/tobeast/generators/PhyloCTMCToBEAST.java

Lines 425 to 432 in 3431219

	// 4. NER
	// ORCNER_Exchange
	Exchange exchange = new Exchange();
	exchange.initByName("tree", tree, "weight", 1.0);
	exchange.setID("ORCNER_Exchange.NER." + tree.getID());
	//TODO disable <operator id="YuleModelNarrow" spec="Exchange" tree="@Tree" weight="0.0"/>