From 8507e6dab2012427f299c069107a49502ef3e24a Mon Sep 17 00:00:00 2001
From: aezarebski <aezarebski@gmail.com>
Date: Mon, 30 Sep 2024 14:50:55 +1000
Subject: [PATCH 1/7] run migrate script on skylinetools clone

---
 src/skylinetools/distributions/BMPrior.java        | 12 ++++++------
 src/skylinetools/distributions/OUPrior.java        | 12 ++++++------
 src/skylinetools/parameter/DateParser.java         |  6 +++---
 .../parameter/RealParameterSequence.java           |  6 +++---
 src/skylinetools/util/TreeDateLogger.java          | 14 +++++++-------
 src/skylinetools/util/TreeDateSlicer.java          |  8 ++++----
 src/skylinetools/util/TreeSliceDateLogger.java     |  8 ++++----
 src/skylinetools/util/TreeSlicer.java              | 10 +++++-----
 .../evolution/speciation/SkylineTimesTest.java     | 12 ++++++------
 test/skylinetools/distributions/OUPriorLkTest.java |  2 +-
 test/skylinetools/util/TreeDateSlicerTest.java     | 10 +++++-----
 test/skylinetools/util/TreeSlicerTest.java         |  4 ++--
 12 files changed, 52 insertions(+), 52 deletions(-)

diff --git a/src/skylinetools/distributions/BMPrior.java b/src/skylinetools/distributions/BMPrior.java
index 64d45f0..30e60ef 100644
--- a/src/skylinetools/distributions/BMPrior.java
+++ b/src/skylinetools/distributions/BMPrior.java
@@ -1,11 +1,11 @@
 package skylinetools.distributions;
 
-import beast.core.Distribution;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.State;
-import beast.core.parameter.RealParameter;
-import beast.math.distributions.ParametricDistribution;
+import beast.base.inference.Distribution;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.inference.State;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.inference.distribution.ParametricDistribution;
 
 import java.util.List;
 import java.util.Random;
diff --git a/src/skylinetools/distributions/OUPrior.java b/src/skylinetools/distributions/OUPrior.java
index 4a452c0..e2e85e0 100644
--- a/src/skylinetools/distributions/OUPrior.java
+++ b/src/skylinetools/distributions/OUPrior.java
@@ -1,11 +1,11 @@
 package skylinetools.distributions;
 
-import beast.core.Distribution;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.State;
-import beast.core.parameter.RealParameter;
-import beast.math.distributions.ParametricDistribution;
+import beast.base.inference.Distribution;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.inference.State;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.inference.distribution.ParametricDistribution;
 
 import java.util.Arrays;
 import java.util.List;
diff --git a/src/skylinetools/parameter/DateParser.java b/src/skylinetools/parameter/DateParser.java
index 5ced97a..1fb2913 100644
--- a/src/skylinetools/parameter/DateParser.java
+++ b/src/skylinetools/parameter/DateParser.java
@@ -1,8 +1,8 @@
 package skylinetools.parameter;
 
-import beast.core.Input;
-import beast.core.parameter.RealParameter;
-import beast.core.util.Log;
+import beast.base.core.Input;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.core.Log;
 
 import java.time.LocalDate;
 import java.time.format.DateTimeFormatter;
diff --git a/src/skylinetools/parameter/RealParameterSequence.java b/src/skylinetools/parameter/RealParameterSequence.java
index c771e2b..9039520 100644
--- a/src/skylinetools/parameter/RealParameterSequence.java
+++ b/src/skylinetools/parameter/RealParameterSequence.java
@@ -1,8 +1,8 @@
 package skylinetools.parameter;
 
-import beast.core.Description;
-import beast.core.Input;
-import beast.core.parameter.RealParameter;
+import beast.base.core.Description;
+import beast.base.core.Input;
+import beast.base.inference.parameter.RealParameter;
 
 import java.util.Arrays;
 
diff --git a/src/skylinetools/util/TreeDateLogger.java b/src/skylinetools/util/TreeDateLogger.java
index d52c2f6..b009947 100644
--- a/src/skylinetools/util/TreeDateLogger.java
+++ b/src/skylinetools/util/TreeDateLogger.java
@@ -1,12 +1,12 @@
 package skylinetools.util;
 
-import beast.core.CalculationNode;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.Loggable;
-import beast.core.parameter.RealParameter;
-import beast.core.util.Log;
-import beast.evolution.tree.Tree;
+import beast.base.inference.CalculationNode;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.core.Loggable;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.core.Log;
+import beast.base.evolution.tree.Tree;
 
 import java.io.PrintStream;
 
diff --git a/src/skylinetools/util/TreeDateSlicer.java b/src/skylinetools/util/TreeDateSlicer.java
index 2be3f76..e764171 100644
--- a/src/skylinetools/util/TreeDateSlicer.java
+++ b/src/skylinetools/util/TreeDateSlicer.java
@@ -1,9 +1,9 @@
 package skylinetools.util;
 
-import beast.core.Function;
-import beast.core.Input;
-import beast.evolution.tree.Tree;
-import beast.util.HeapSort;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.evolution.tree.Tree;
+import beast.base.util.HeapSort;
 
 import java.util.Arrays;
 
diff --git a/src/skylinetools/util/TreeSliceDateLogger.java b/src/skylinetools/util/TreeSliceDateLogger.java
index ddb6942..6c49816 100644
--- a/src/skylinetools/util/TreeSliceDateLogger.java
+++ b/src/skylinetools/util/TreeSliceDateLogger.java
@@ -1,9 +1,9 @@
 package skylinetools.util;
 
-import beast.core.CalculationNode;
-import beast.core.Function;
-import beast.core.Input;
-import beast.core.Loggable;
+import beast.base.inference.CalculationNode;
+import beast.base.core.Function;
+import beast.base.core.Input;
+import beast.base.core.Loggable;
 
 import java.io.PrintStream;
 
diff --git a/src/skylinetools/util/TreeSlicer.java b/src/skylinetools/util/TreeSlicer.java
index adb1b23..33a1ef4 100644
--- a/src/skylinetools/util/TreeSlicer.java
+++ b/src/skylinetools/util/TreeSlicer.java
@@ -1,11 +1,11 @@
 package skylinetools.util;
 
 import beast.core.*;
-import beast.core.parameter.Parameter;
-import beast.core.parameter.RealParameter;
-import beast.evolution.tree.Node;
-import beast.evolution.tree.Tree;
-import beast.util.HeapSort;
+import beast.base.inference.parameter.Parameter;
+import beast.base.inference.parameter.RealParameter;
+import beast.base.evolution.tree.Node;
+import beast.base.evolution.tree.Tree;
+import beast.base.util.HeapSort;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/test/beast/evolution/speciation/SkylineTimesTest.java b/test/beast/evolution/speciation/SkylineTimesTest.java
index 42b881f..c47aa65 100755
--- a/test/beast/evolution/speciation/SkylineTimesTest.java
+++ b/test/beast/evolution/speciation/SkylineTimesTest.java
@@ -1,17 +1,17 @@
 package beast.evolution.speciation;
 
-import beast.core.parameter.BooleanParameter;
-import beast.core.parameter.RealParameter;
-import beast.evolution.speciation.BirthDeathSkylineModelTestHelper;
-import beast.evolution.tree.Tree;
-import beast.util.TreeParser;
+import beast.base.inference.parameter.BooleanParameter;
+import beast.base.inference.parameter.RealParameter;
+import bdsky.evolution.speciation.BirthDeathSkylineModelTestHelper;
+import beast.base.evolution.tree.Tree;
+import beast.base.evolution.tree.TreeParser;
 import org.junit.Test;
 import junit.framework.TestCase;
 
 import java.util.List;
 
 /**
- * This test is to check how bdsky (beast.evolution.speciation.BirthDeathSkylineModel) sets change-point times, depending
+ * This test is to check how bdsky (bdsky.evolution.speciation.BirthDeathSkylineModel) sets change-point times, depending
  * on the input.
  *
  * There are 5 different ways to set the change-point times:
diff --git a/test/skylinetools/distributions/OUPriorLkTest.java b/test/skylinetools/distributions/OUPriorLkTest.java
index 4fb983a..663027c 100644
--- a/test/skylinetools/distributions/OUPriorLkTest.java
+++ b/test/skylinetools/distributions/OUPriorLkTest.java
@@ -1,6 +1,6 @@
 package skylinetools.distributions;
 
-import beast.core.parameter.RealParameter;
+import beast.base.inference.parameter.RealParameter;
 import junit.framework.TestCase;
 import org.junit.Test;
 import skylinetools.distributions.OUPrior;
diff --git a/test/skylinetools/util/TreeDateSlicerTest.java b/test/skylinetools/util/TreeDateSlicerTest.java
index 12be810..305b5be 100644
--- a/test/skylinetools/util/TreeDateSlicerTest.java
+++ b/test/skylinetools/util/TreeDateSlicerTest.java
@@ -1,10 +1,10 @@
 package skylinetools.util;
 
-import beast.evolution.alignment.Taxon;
-import beast.evolution.alignment.TaxonSet;
-import beast.evolution.tree.TraitSet;
-import beast.evolution.tree.Tree;
-import beast.util.TreeParser;
+import beast.base.evolution.alignment.Taxon;
+import beast.base.evolution.alignment.TaxonSet;
+import beast.base.evolution.tree.TraitSet;
+import beast.base.evolution.tree.Tree;
+import beast.base.evolution.tree.TreeParser;
 import junit.framework.TestCase;
 import org.junit.Test;
 import skylinetools.parameter.DateParser;
diff --git a/test/skylinetools/util/TreeSlicerTest.java b/test/skylinetools/util/TreeSlicerTest.java
index 61c0e46..4613fff 100644
--- a/test/skylinetools/util/TreeSlicerTest.java
+++ b/test/skylinetools/util/TreeSlicerTest.java
@@ -1,7 +1,7 @@
 package skylinetools.util;
 
-import beast.evolution.tree.Tree;
-import beast.util.TreeParser;
+import beast.base.evolution.tree.Tree;
+import beast.base.evolution.tree.TreeParser;
 import junit.framework.TestCase;
 import org.junit.Test;
 import test.beast.BEASTTestCase;

From a49ae843cf5ac92beead329b9c089a83b8438e3b Mon Sep 17 00:00:00 2001
From: aezarebski <aezarebski@gmail.com>
Date: Mon, 30 Sep 2024 15:04:57 +1000
Subject: [PATCH 2/7] fix a couple of imports merge.pl seems to have missed

---
 .../evolution/speciation/BirthDeathSkylineModelTestHelper.java | 3 ++-
 src/skylinetools/util/TreeSlicer.java                          | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/beast/evolution/speciation/BirthDeathSkylineModelTestHelper.java b/src/beast/evolution/speciation/BirthDeathSkylineModelTestHelper.java
index 470e567..38dfe57 100755
--- a/src/beast/evolution/speciation/BirthDeathSkylineModelTestHelper.java
+++ b/src/beast/evolution/speciation/BirthDeathSkylineModelTestHelper.java
@@ -1,5 +1,6 @@
 package beast.evolution.speciation;
 
+import bdsky.evolution.speciation.BirthDeathSkylineModel;
 import java.util.List;
 
 /**
@@ -17,4 +18,4 @@ public class BirthDeathSkylineModelTestHelper extends BirthDeathSkylineModel {
 
     public List<Double> rChangeTimes() { return rChangeTimes; }
 
-}
\ No newline at end of file
+}
diff --git a/src/skylinetools/util/TreeSlicer.java b/src/skylinetools/util/TreeSlicer.java
index 33a1ef4..7923f92 100644
--- a/src/skylinetools/util/TreeSlicer.java
+++ b/src/skylinetools/util/TreeSlicer.java
@@ -1,6 +1,6 @@
 package skylinetools.util;
 
-import beast.core.*;
+import beast.base.core.*;
 import beast.base.inference.parameter.Parameter;
 import beast.base.inference.parameter.RealParameter;
 import beast.base.evolution.tree.Node;

From 4495beac2440129c9450c0ed51ee316b393d6441 Mon Sep 17 00:00:00 2001
From: aezarebski <aezarebski@gmail.com>
Date: Mon, 30 Sep 2024 15:05:18 +1000
Subject: [PATCH 3/7] update versions in build.xml and version.xml

---
 build.xml   | 2 +-
 version.xml | 5 ++---
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/build.xml b/build.xml
index 85ee2c0..fc1685d 100644
--- a/build.xml
+++ b/build.xml
@@ -117,7 +117,7 @@
       <echo>Downloading dependencies...</echo>
 
       <echo>BDSKY:</echo>
-      <get src="https://github.com/BEAST2-Dev/bdsky/releases/download/1.4.0/BDSKY.addon.1.4.0.zip"
+      <get src="https://github.com/BEAST2-Dev/bdsky/releases/download/v1.5.0/BDSKY.v1.5.0.zip"
            dest="${build-lib}/BDSKY.zip"/>
       <mkdir dir="${build-lib}/BDSKY"/>
       <unzip src="${build-lib}/BDSKY.zip" dest="${build-lib}/BDSKY"/>
diff --git a/version.xml b/version.xml
index 7311e37..5d70289 100644
--- a/version.xml
+++ b/version.xml
@@ -1,7 +1,6 @@
 <addon name="skylinetools" version="0.2.0">
-            <depends on="beast2" atleast="2.5.0"/>
-            <depends on="BDSKY" atleast="1.4.0"/>
+            <depends on="beast2" atleast="2.7.0"/>
+            <depends on="BDSKY" atleast="1.5.0"/>
 
             <!-- Add other dependencies as necessary. -->
             </addon>
-        

From 360f836ec84002ffb5775caedfcc81aac17b836a Mon Sep 17 00:00:00 2001
From: aezarebski <aezarebski@gmail.com>
Date: Mon, 30 Sep 2024 16:45:58 +1000
Subject: [PATCH 4/7] fix typo that beauti found

---
 version.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/version.xml b/version.xml
index 5d70289..0da708b 100644
--- a/version.xml
+++ b/version.xml
@@ -1,6 +1,7 @@
 <addon name="skylinetools" version="0.2.0">
-            <depends on="beast2" atleast="2.7.0"/>
             <depends on="BDSKY" atleast="1.5.0"/>
+	<depends on='BEAST.base' atleast='2.7.2'/>
+	<depends on='BEAST.app' atleast='2.7.2'/>
 
             <!-- Add other dependencies as necessary. -->
             </addon>

From f7ca7996cd50fb1e8cb6ac4c7bd64b0940f23532 Mon Sep 17 00:00:00 2001
From: aezarebski <aezarebski@gmail.com>
Date: Mon, 30 Sep 2024 16:46:20 +1000
Subject: [PATCH 5/7] bump minor to avoid confusion with previous versions

---
 version.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/version.xml b/version.xml
index 0da708b..2f35383 100644
--- a/version.xml
+++ b/version.xml
@@ -1,4 +1,4 @@
-<addon name="skylinetools" version="0.2.0">
+<addon name="skylinetools" version="0.3.0">
             <depends on="BDSKY" atleast="1.5.0"/>
 	<depends on='BEAST.base' atleast='2.7.2'/>
 	<depends on='BEAST.app' atleast='2.7.2'/>

From 2466c201fd293bf59730a7fbb3802930627163fa Mon Sep 17 00:00:00 2001
From: aezarebski <aezarebski@gmail.com>
Date: Mon, 30 Sep 2024 17:09:35 +1000
Subject: [PATCH 6/7] couple more tweaks to get beauti to play nicely

---
 build.xml   |  4 ++--
 version.xml | 14 +++++++++-----
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/build.xml b/build.xml
index fc1685d..12a3c99 100644
--- a/build.xml
+++ b/build.xml
@@ -191,7 +191,7 @@
 
         <mkdir dir="${pack}"/>
         <mkdir dir="${pack}/examples"/>
-        <mkdir dir="${pack}/templates"/>
+        <mkdir dir="${pack}/fxtemplates"/>
         <mkdir dir="${pack}/lib"/>
         <mkdir dir="${pack}/doc"/>
 
@@ -217,7 +217,7 @@
         </copy>
 
         <mkdir dir="${templates}" />
-        <copy todir="${pack}/templates">
+        <copy todir="${pack}/fxtemplates">
             <fileset dir="${templates}" includes="*.xml" />
         </copy>
 
diff --git a/version.xml b/version.xml
index 2f35383..3b29826 100644
--- a/version.xml
+++ b/version.xml
@@ -1,7 +1,11 @@
 <addon name="skylinetools" version="0.3.0">
-            <depends on="BDSKY" atleast="1.5.0"/>
-	<depends on='BEAST.base' atleast='2.7.2'/>
-	<depends on='BEAST.app' atleast='2.7.2'/>
+  <depends on="BDSKY" atleast="1.5.0"/>
+  <depends on='BEAST.base' atleast='2.7.2'/>
+  <depends on='BEAST.app' atleast='2.7.2'/>
 
-            <!-- Add other dependencies as necessary. -->
-            </addon>
+  <!-- Add other dependencies as necessary. -->
+
+  <service type="beast.base.core.BEASTInterface">
+    <provider classname="skylinetools.distributions.BMPrior"/>
+  </service>
+</addon>

From efa4f78956f11cd5cb29c839e115609a0aed2dcb Mon Sep 17 00:00:00 2001
From: aezarebski <aezarebski@gmail.com>
Date: Mon, 30 Sep 2024 17:10:38 +1000
Subject: [PATCH 7/7] run migrate on example scripts

---
 .../smoothingpriors/comparison/hcv_bdsky.xml  | 44 +++++++++----------
 examples/smoothingpriors/ouprior_test1.xml    |  2 +-
 examples/smoothingpriors/ouprior_test2.xml    |  2 +-
 examples/smoothingpriors/ouprior_test3.xml    | 24 +++++-----
 examples/smoothingpriors/ouprior_test4.xml    | 22 +++++-----
 examples/smoothingpriors/ouprior_test5.xml    |  2 +-
 6 files changed, 48 insertions(+), 48 deletions(-)

diff --git a/examples/smoothingpriors/comparison/hcv_bdsky.xml b/examples/smoothingpriors/comparison/hcv_bdsky.xml
index 3586c09..cb78bdf 100644
--- a/examples/smoothingpriors/comparison/hcv_bdsky.xml
+++ b/examples/smoothingpriors/comparison/hcv_bdsky.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<beast beautitemplate='Standard' beautistatus='' namespace="beast.core
+<beast beautitemplate='Standard' beautistatus='' namespace="beast.pkgmgmt:beast.base.core:beast.base.inference
                                                            :beast.evolution.alignment
                                                            :beast.evolution.tree.coalescent
                                                            :beast.core.util
@@ -12,16 +12,16 @@
 
 
 
-<map name="Uniform" >beast.math.distributions.Uniform</map>
-<map name="Exponential" >beast.math.distributions.Exponential</map>
-<map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
-<map name="Normal" >beast.math.distributions.Normal</map>
-<map name="Beta" >beast.math.distributions.Beta</map>
-<map name="Gamma" >beast.math.distributions.Gamma</map>
-<map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
-<map name="prior" >beast.math.distributions.Prior</map>
-<map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
-<map name="OneOnX" >beast.math.distributions.OneOnX</map>
+<map name="Uniform" >beast.base.inference.distribution.Uniform</map>
+<map name="Exponential" >beast.base.inference.distribution.Exponential</map>
+<map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
+<map name="Normal" >beast.base.inference.distribution.Normal</map>
+<map name="Beta" >beast.base.inference.distribution.Beta</map>
+<map name="Gamma" >beast.base.inference.distribution.Gamma</map>
+<map name="LaplaceDistribution" >beast.base.inference.distribution.LaplaceDistribution</map>
+<map name="prior" >beast.base.inference.distribution.Prior</map>
+<map name="InverseGamma" >beast.base.inference.distribution.InverseGamma</map>
+<map name="OneOnX" >beast.base.inference.distribution.OneOnX</map>
 
 
 <data id="hcv" name="alignment">
@@ -119,21 +119,21 @@
     </state>
 
     <!-- Initial tree -->
-    <init id="RandomTree.t:hcv" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:hcv" taxa="@hcv">
+    <init id="RandomTree.t:hcv" spec="beast.base.evolution.tree.coalescent.RandomTree" estimate="false" initial="@Tree.t:hcv" taxa="@hcv">
         <populationModel id="ConstantPopulation0.t:hcv" spec="ConstantPopulation">
             <parameter id="randomPopSize.t:hcv" name="popSize">1.0</parameter>
         </populationModel>
     </init>
 
 
-    <distribution id="posterior" spec="util.CompoundDistribution">
+    <distribution id="posterior" spec="beast.base.inference.CompoundDistribution">
 
           <!-- Begin prior -->
-          <distribution id="prior" spec="util.CompoundDistribution">
+          <distribution id="prior" spec="beast.base.inference.CompoundDistribution">
 
                <!-- Treeprior (BDSKY contemporary) -->
                <distribution id="BirthDeathSkyContemporary.t:hcv" 
-                             spec="beast.evolution.speciation.BirthDeathSkylineModel" 
+                             spec="bdsky.evolution.speciation.BirthDeathSkylineModel" 
                              tree="@Tree.t:hcv"
                              reproductiveNumber="@reproductiveNumber.t:hcv" 
                              becomeUninfectiousRate="@becomeUninfectiousRate.t:hcv"                                                           
@@ -186,7 +186,7 @@
 
 
           <!-- Begin likelihood -->
-          <distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
+          <distribution id="likelihood" spec="beast.base.inference.CompoundDistribution" useThreads="true">
 
                <!-- Alignment likelihood -->
                <distribution id="treeLikelihood.hcv" spec="ThreadedTreeLikelihood" data="@hcv" tree="@Tree.t:hcv">
@@ -202,7 +202,7 @@
                     </siteModel>
 
                     <!-- Clock model (fixed clock-rate) -->
-                    <branchRateModel id="StrictClock.c:hcv" spec="beast.evolution.branchratemodel.StrictClockModel">
+                    <branchRateModel id="StrictClock.c:hcv" spec="beast.base.evolution.branchratemodel.StrictClockModel">
                          <parameter id="clockRate.c:hcv" estimate="false" name="clock.rate">7.9E-4</parameter>
                     </branchRateModel>
 
@@ -267,21 +267,21 @@
         <log idref="rateGT.s:hcv"/>
         <log idref="freqParameter.s:hcv"/>
 
-        <log id="TreeHeight.t:hcv" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:hcv"/>        
+        <log id="TreeHeight.t:hcv" spec="beast.base.evolution.tree.TreeHeightLogger" tree="@Tree.t:hcv"/>        
         <log idref="origin.t:hcv"/>
         <log idref="reproductiveNumber.t:hcv"/>        
         <log idref="becomeUninfectiousRate.t:hcv"/>
         <log idref="rho.t:hcv"/>
         
-        <log id="birth.t:hcv" spec="beast.math.statistic.RPNcalculator" expression="reproductiveNumber.t:hcv becomeUninfectiousRate.t:hcv *">
+        <log id="birth.t:hcv" spec="beast.base.inference.util.RPNcalculator" expression="reproductiveNumber.t:hcv becomeUninfectiousRate.t:hcv *">
             <parameter idref="becomeUninfectiousRate.t:hcv"/>
             <parameter idref="reproductiveNumber.t:hcv"/>
         </log>
-        <log id="death.t:hcv" spec="beast.math.statistic.RPNcalculator" expression="becomeUninfectiousRate.t:hcv 1 samplingProportion.t:hcv - *">
+        <log id="death.t:hcv" spec="beast.base.inference.util.RPNcalculator" expression="becomeUninfectiousRate.t:hcv 1 samplingProportion.t:hcv - *">
             <parameter idref="becomeUninfectiousRate.t:hcv"/>
             <parameter idref="samplingProportion.t:hcv"/>
         </log>
-        <log id="sampling.t:hcv" spec="beast.math.statistic.RPNcalculator" expression="becomeUninfectiousRate.t:hcv samplingProportion.t:hcv *">
+        <log id="sampling.t:hcv" spec="beast.base.inference.util.RPNcalculator" expression="becomeUninfectiousRate.t:hcv samplingProportion.t:hcv *">
             <parameter idref="becomeUninfectiousRate.t:hcv"/>
             <parameter idref="samplingProportion.t:hcv"/>
         </log>
@@ -295,7 +295,7 @@
     </logger>
 
     <!--logger id="treelog.t:hcv" fileName="hcv_bdsky_$(tree).trees" logEvery="4000" mode="tree">
-        <log id="TreeWithMetaDataLogger.t:hcv" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:hcv"/>
+        <log id="TreeWithMetaDataLogger.t:hcv" spec="beast.base.evolution.TreeWithMetaDataLogger" tree="@Tree.t:hcv"/>
     </logger-->
 
 </run>
diff --git a/examples/smoothingpriors/ouprior_test1.xml b/examples/smoothingpriors/ouprior_test1.xml
index 7bc36a6..f45283a 100644
--- a/examples/smoothingpriors/ouprior_test1.xml
+++ b/examples/smoothingpriors/ouprior_test1.xml
@@ -1,5 +1,5 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->
 
diff --git a/examples/smoothingpriors/ouprior_test2.xml b/examples/smoothingpriors/ouprior_test2.xml
index 1b11c9a..21ca903 100644
--- a/examples/smoothingpriors/ouprior_test2.xml
+++ b/examples/smoothingpriors/ouprior_test2.xml
@@ -1,5 +1,5 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->
 
diff --git a/examples/smoothingpriors/ouprior_test3.xml b/examples/smoothingpriors/ouprior_test3.xml
index acfae63..b06e991 100644
--- a/examples/smoothingpriors/ouprior_test3.xml
+++ b/examples/smoothingpriors/ouprior_test3.xml
@@ -1,18 +1,18 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->
 
-    <map name="Uniform" >beast.math.distributions.Uniform</map>
-    <map name="Exponential" >beast.math.distributions.Exponential</map>
-    <map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
-    <map name="Normal" >beast.math.distributions.Normal</map>
-    <map name="Beta" >beast.math.distributions.Beta</map>
-    <map name="Gamma" >beast.math.distributions.Gamma</map>
-    <map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
-    <map name="prior" >beast.math.distributions.Prior</map>
-    <map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
-    <map name="OneOnX" >beast.math.distributions.OneOnX</map>
+    <map name="Uniform" >beast.base.inference.distribution.Uniform</map>
+    <map name="Exponential" >beast.base.inference.distribution.Exponential</map>
+    <map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Normal" >beast.base.inference.distribution.Normal</map>
+    <map name="Beta" >beast.base.inference.distribution.Beta</map>
+    <map name="Gamma" >beast.base.inference.distribution.Gamma</map>
+    <map name="LaplaceDistribution" >beast.base.inference.distribution.LaplaceDistribution</map>
+    <map name="prior" >beast.base.inference.distribution.Prior</map>
+    <map name="InverseGamma" >beast.base.inference.distribution.InverseGamma</map>
+    <map name="OneOnX" >beast.base.inference.distribution.OneOnX</map>
 
     <run spec="MCMC" id="mcmc" chainLength="10000000"> <!--autoOptimize="true"-->
         <state>
@@ -29,7 +29,7 @@
                 <parameter spec='RealParameter' name='mean' id='mu' dimension="1" value="1"/>
                 <parameter spec='RealParameter' name='sigma' id='sigma' dimension="1" value="0.5"/>
                 <parameter spec='RealParameter' name='nu' id='nu' dimension="1" value="0.1"/>
-                <distribution spec='beast.math.distributions.Uniform' name="x0Prior" lower="1.5" upper="2.5"/>
+                <distribution spec='beast.base.inference.distribution.Uniform' name="x0Prior" lower="1.5" upper="2.5"/>
             </distribution>
 
             <prior id="muPrior" name="distribution" x="@mu">                      
diff --git a/examples/smoothingpriors/ouprior_test4.xml b/examples/smoothingpriors/ouprior_test4.xml
index 88e8421..b7423be 100644
--- a/examples/smoothingpriors/ouprior_test4.xml
+++ b/examples/smoothingpriors/ouprior_test4.xml
@@ -1,18 +1,18 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions:skylinetools.parameter'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions:skylinetools.parameter'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->
 
-    <map name="Uniform" >beast.math.distributions.Uniform</map>
-    <map name="Exponential" >beast.math.distributions.Exponential</map>
-    <map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
-    <map name="Normal" >beast.math.distributions.Normal</map>
-    <map name="Beta" >beast.math.distributions.Beta</map>
-    <map name="Gamma" >beast.math.distributions.Gamma</map>
-    <map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
-    <map name="prior" >beast.math.distributions.Prior</map>
-    <map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
-    <map name="OneOnX" >beast.math.distributions.OneOnX</map>
+    <map name="Uniform" >beast.base.inference.distribution.Uniform</map>
+    <map name="Exponential" >beast.base.inference.distribution.Exponential</map>
+    <map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
+    <map name="Normal" >beast.base.inference.distribution.Normal</map>
+    <map name="Beta" >beast.base.inference.distribution.Beta</map>
+    <map name="Gamma" >beast.base.inference.distribution.Gamma</map>
+    <map name="LaplaceDistribution" >beast.base.inference.distribution.LaplaceDistribution</map>
+    <map name="prior" >beast.base.inference.distribution.Prior</map>
+    <map name="InverseGamma" >beast.base.inference.distribution.InverseGamma</map>
+    <map name="OneOnX" >beast.base.inference.distribution.OneOnX</map>
 
     <run spec="MCMC" id="mcmc" chainLength="200000000"> <!--autoOptimize="true"-->
         <state>
diff --git a/examples/smoothingpriors/ouprior_test5.xml b/examples/smoothingpriors/ouprior_test5.xml
index f1fde50..94eb793 100644
--- a/examples/smoothingpriors/ouprior_test5.xml
+++ b/examples/smoothingpriors/ouprior_test5.xml
@@ -1,5 +1,5 @@
 <beast version='2.0'
-       namespace='beast.core:beast.evolution.speciation:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.math.distributions:beast.evolution.branchratemodel:beast.evolution.likelihood:beast.core.parameter:skylinetools.distributions:skylinetools.parameter'>
+       namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions:skylinetools.parameter'>
 
     <!-- Test XML for the Ornstein-Uhlenbeck prior -->