Merge branch 'master' into auto_version

.gitignore

@@ -16,4 +16,5 @@ out/
 !ci/**/*.xml
 
 zig_zag
-src/revision.txt
+src/revision.txt
+*.dmg

build.xml

@@ -101,7 +101,8 @@
                fork="true"
                includeantruntime="false"
                memoryinitialsize="256m"
-               memorymaximumsize="1024m">
+               memorymaximumsize="1024m"
+               encoding="UTF-8">
             <include name="dr/app/beast/**"/>
             <include name="dr/app/beauti/**"/>
             <include name="dr/app/bss/**"/>
@@ -230,13 +231,14 @@
                 <include name="dr/evomodel/branchratemodel/**/*.class"/>
                 <include name="dr/evomodel/clock/**/*.class"/>
                 <include name="dr/evomodel/coalescent/**/*.class"/>
+                <include name="dr/evomodel/continuous/**/*.class"/>
                 <include name="dr/evomodel/operators/**/*.class"/>
                 <include name="dr/evomodel/sitemodel/**/*.class"/>
                 <include name="dr/evomodel/speciation/**/*.class"/>
                 <include name="dr/evomodel/substmodel/**/*.class"/>
                 <include name="dr/evomodel/tree/**/*.class"/>
                 <include name="dr/evomodel/treelikelihood/**/*.class"/>
-                <exclude name="dr/evomodel/treedatalikelihood/MultiPartitionDataLikelihoodDelegate*"/>
+                <include name="dr/evomodel/treedatalikelihood/**/*.class"/>
                 <include name="dr/evomodelxml/**/*.class"/>
                 <exclude name="dr/evomodelxml/treedatalikelihood/MultiPartitionDataLikelihoodDelegate*"/>
                 <include name="dr/evoxml/**/*.class"/>
@@ -283,13 +285,38 @@
             </fileset>
         </jar>
 
+        <!-- Put everything in ${build} into the tempest-lib.jar file -->
+        <jar jarfile="${dist}/tempest-lib.jar">
+            <manifest>
+                <attribute name="Built-By" value="${user.name}"/>
+            </manifest>
+            <fileset dir="${build}">
+                <include name="dr/app/beauti/tipdatepanel/**/*.class"/>
+                <include name="dr/app/beauti/util/**/*.class"/>
+                <include name="dr/app/beauti/options/**/*.class"/>
+                <include name="dr/app/gui/**/*.class"/>
+                <include name="dr/app/tools/*.class"/>
+                <include name="dr/app/util/*.class"/>
+                <include name="dr/evolution/tree/**/*.class"/>
+                <include name="dr/evolution/io/*.class"/>
+                <include name="dr/evolution/util/*.class"/>
+                <include name="dr/math/**/*.class"/>
+                <include name="dr/stats/**/*.class"/>
+                <include name="dr/util/**/*.class"/>
+            </fileset>
+        </jar>
     </target>
 
     <!-- used to copy the compiled trace.jar into place in the Tracer lib folder -->
     <target name="copy_trace_jar" depends="dist" >
         <copy file="${dist}/trace.jar" todir="../Tracer/lib"/>
     </target>
 
+    <!-- used to copy the compiled tempest-lib.jar into place in the Tempest lib folder -->
+    <target name="copy_tempest-lib_jar" depends="dist" >
+        <copy file="${dist}/tempest-lib.jar" todir="../Tempest/lib"/>
+    </target>
+
     <!-- run beast.jar -->
     <target name="run_BEAST">
         <java jar="${dist}/beast.jar" fork="true"/>
@@ -690,7 +717,7 @@
 					useJavaXKey="true"
                     icon="${common_dir}/icons/beast.icns"
                     jvmversion="${jvm_version}"
-                    vmoptions="-Xmx2048M"
+                    vmoptions="-Xmx2048M -Djava.library.path=/usr/local/lib"
                     arguments="-window -working -options"
                     highresolutioncapable="true"
                     version="${version}"

build_coalsim.xml

@@ -8,7 +8,7 @@
     <property name="build" location="build"/>
     <property name="lib" location="lib"/>
     <property name="dist" location="dist"/>
-                                                                                2
+
     <property environment="env"/>
 
     <target name="init">