diff --git a/build.xml b/build.xml
deleted file mode 100644
index fd0801bfb..000000000
--- a/build.xml
+++ /dev/null
@@ -1,1518 +0,0 @@
-<!--
-  ~ Copyright (c) 2012, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<!-- To get a list of the major build targets, run "ant -p" -->
-<project name="Sting" default="dist" basedir="."
-         xmlns:artifact="antlib:org.apache.maven.artifact.ant"
-         xmlns:ivy="antlib:org.apache.ivy.ant">
-    <description>Compile and distribute the Sting toolkit</description>
-
-    <!-- ******************************************************************************** -->
-    <!-- Properties                                                                       -->
-    <!-- ******************************************************************************** -->
-
-    <!-- The system classpath should take precedence over classpaths specified in this file -->
-    <property name="build.sysclasspath" value="first" />
-
-    <!-- Use this prefix to access environment variables -->
-    <property environment="env"/>
-
-    <!-- Build defaults: -->
-    <property name="default.build.target" value="all" />       <!-- can be "all", "public" (public only), or "protected" (public + protected) -->
-    <property name="compile.scala.by.default" value="true" />  <!-- compile Scala by default? "true" or "false" -->
-    <property name="use.contracts.by.default" value="false" /> <!-- should contracts be built by default? "true" or "false -->
-
-    <!-- Top-level directories -->
-    <property name="build.dir" value="build" />
-    <property name="dist.dir" value="dist" />
-    <property name="lib.dir" value="lib" />
-    <property name="public.dir" value="public" />
-    <property name="private.dir" value="private" />
-    <property name="protected.dir" value="protected" />
-    <property name="external.dir" value="external" />
-
-    <!-- Source directories -->
-    <property name="java.public.source.dir" value="${public.dir}/java/src" />
-    <property name="java.private.source.dir" value="${private.dir}/java/src" />
-    <property name="java.protected.source.dir" value="${protected.dir}/java/src" />
-    <property name="scala.public.source.dir" value="${public.dir}/scala/src" />
-    <property name="scala.private.source.dir" value="${private.dir}/scala/src" />
-    <property name="scala.protected.source.dir" value="${protected.dir}/scala/src" />
-    <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
-    <property name="R.public.scripts.dir" value="${public.dir}/R/scripts" />
-    <property name="R.private.scripts.dir" value="${private.dir}/R/scripts" />
-    <property name="R.protected.scripts.dir" value="${protected.dir}/R/scripts" />
-    <property name="R.public.src.dir" value="${public.dir}/R/src" />
-
-    <!-- Build directories -->
-    <property name="java.classes" value="${build.dir}/java/classes" />
-    <property name="scala.classes" value="${build.dir}/scala/classes" />
-    <property name="R.library.dir" value="${public.dir}/R" />  <!-- TODO: Installing libraries back into the source directory: intentionally avoids ant clean?? -->
-    <property name="R.tar.dir" value="${build.dir}/R/src" />
-    <property name="R.package.path" value="org/broadinstitute/sting/utils/R" />
-    <property name="R.script.staging.dir" value="${build.dir}/R/stage" />
-
-    <!-- Packaging system properties -->
-    <property name="package.xml.dir" value="${public.dir}/packages" />
-    <property name="package.output.dir" value="${dist.dir}/packages" />
-    <property name="staging.dir" value="staging" />
-    <property name="default.executable" value="none" />
-
-    <!-- GATKDocs/Javadoc/Scaladoc directories -->
-    <property name="gatkdocs.dir" value="gatkdocs" />
-    <property name="javadoc.dir" value="javadoc" />
-    <property name="scaladoc.dir" value="scaladoc" />
-
-    <!-- Resource file used for help text and version information -->
-    <property name="resource.file" value="StingText.properties" />
-    <property name="resource.path" value="${java.classes}/StingText.properties" />
-
-    <!-- Directory containing cryptographic keys used by the GATK -->
-    <property name="key.dir" value="${public.dir}/keys" />
-
-    <!-- Contracts for Java -->
-    <!-- Disabled by default -->
-    <!-- To enable, run with -Duse.contracts=true -->
-    <property name="java.contracts.dir" value="${build.dir}/java/contracts" />
-    <property name="contracts.version" value="1.0-r139" />
-    <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
-    <property name="contract.dump.dir" value="dump" />
-
-    <!-- do we want to halt on failure of a unit test? default to yes (Bamboo uses 'no') -->
-    <property name="halt" value="yes" />
-
-    <!-- should our unit test output go to a file or the screen? false means it goes to the screen (default) true to file -->
-    <property name="usefile" value="false" />
-
-    <!-- To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
-    <property name="test.debug.port" value="5005" />  <!-- override on the command line if desired -->
-    <property name="test.default.maxmemory" value="4g"/>
-
-    <!-- clover parameters -->
-    <property name="clover.jar" location="private/resources/clover/lib/clover.jar"/>
-    <property name="clover.instrument.level" value="method"/>
-    <taskdef resource="cloverlib.xml" classpath="${clover.jar}"/>
-
-    <!-- ******************************************************************************** -->
-    <!-- Filesets and paths                                                               -->
-    <!-- ******************************************************************************** -->
-
-    <!-- All the complexity of selecting among public/private/protected should be up here, not down in the targets -->
-
-    <patternset id="java.source.directories.pattern">
-        <include name="${java.public.source.dir}" />
-        <include name="${java.private.source.dir}" if="include.private" />
-        <include name="${java.protected.source.dir}" if="include.protected" />
-    </patternset>
-
-    <patternset id="java.source.files.pattern">
-        <include name="${java.public.source.dir}/**/*.java" />
-        <include name="${java.private.source.dir}/**/*.java" if="include.private" />
-        <include name="${java.protected.source.dir}/**/*.java" if="include.protected" />
-    </patternset>
-
-    <patternset id="scala.source.directories.pattern">
-        <include name="${scala.public.source.dir}" />
-        <include name="${scala.private.source.dir}" if="include.private" />
-        <include name="${scala.protected.source.dir}" if="include.protected" />
-    </patternset>
-
-    <patternset id="scala.source.files.pattern">
-        <include name="${scala.public.source.dir}/**/*.scala" />
-        <include name="${scala.private.source.dir}/**/*.scala" if="include.private" />
-        <include name="${scala.protected.source.dir}/**/*.scala" if="include.protected" />
-    </patternset>
-
-    <patternset id="R.script.source.directories.pattern">
-        <include name="${R.public.scripts.dir}" />
-        <include name="${R.private.scripts.dir}" if="include.private" />
-        <include name="${R.protected.scripts.dir}" if="include.protected" />
-    </patternset>
-
-    <patternset id="R.script.source.files.pattern">
-        <include name="${R.public.scripts.dir}/**/*.R" />
-        <include name="${R.private.scripts.dir}/**/*.R" if="include.private" />
-        <include name="${R.protected.scripts.dir}/**.*.R" if="include.protected" />
-    </patternset>
-
-    <path id="java.source.path">
-        <dirset dir="${basedir}">
-            <patternset refid="java.source.directories.pattern" />
-        </dirset>
-    </path>
-
-    <path id="scala.source.path">
-        <dirset dir="${basedir}">
-            <patternset refid="scala.source.directories.pattern" />
-        </dirset>
-    </path>
-
-    <path id="R.script.source.path">
-        <dirset dir="${basedir}">
-            <patternset refid="R.script.source.directories.pattern" />
-        </dirset>
-    </path>
-
-    <fileset id="java.source.files" dir="${basedir}">
-        <patternset refid="java.source.files.pattern" />
-    </fileset>
-
-    <fileset id="scala.source.files" dir="${basedir}">
-        <patternset refid="scala.source.files.pattern" />
-    </fileset>
-
-    <fileset id="R.script.source.files" dir="${basedir}">
-        <patternset refid="R.script.source.files.pattern" />
-    </fileset>
-
-    <fileset id="java.class.files" dir="${java.classes}" erroronmissingdir="false">
-        <include name="**/*.class"/>
-    </fileset>
-
-    <patternset id="dependency.mask" includes="*.jar" />
-
-    <path id="external.dependencies">
-        <fileset dir="${lib.dir}" erroronmissingdir="false">
-            <patternset refid="dependency.mask" />
-        </fileset>
-    </path>
-
-    <path id="scala.dependencies">
-        <path refid="external.dependencies" />
-        <pathelement location="${java.classes}" />
-        <!-- Need the resources as we will be running a command line program which needs the help text. -->
-        <pathelement location="${resource.path}" />
-        <!-- Add any previously compiled scala classes to the path. -->
-        <pathelement location="${scala.classes}" />
-    </path>
-
-    <path id="build.results">
-        <!-- Ensure that GenomeAnalysisTK.jar comes first in the path, as it contains overrides for certain classes in our dependencies -->
-        <pathelement location="${dist.dir}/GenomeAnalysisTK.jar" />
-        <!-- After GenomeAnalysisTK.jar we include all of the other jars in the dist directory -->
-        <fileset dir="${dist.dir}" erroronmissingdir="false">
-            <patternset refid="dependency.mask" />
-            <exclude name="GenomeAnalysisTK.jar" />
-        </fileset>
-    </path>
-
-    <fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
-        <include name="**/*.java" />
-    </fileset>
-
-    <path id="external.build.dir">
-        <path path="${java.classes}" />
-    </path>
-
-    <path id="external.dist.dir">
-        <path path="${dist.dir}" />
-    </path>
-
-    <!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
-    <path id="external.gatk.classpath">
-        <path path="${java.classes}"/>
-        <path refid="external.dependencies" />
-    </path>
-
-    <!-- the path for resources that need to go into the GATK jar;
-         any additional resources should go into this set. -->
-    <path id="gatk.resources">
-        <fileset dir="${java.public.source.dir}">
-            <include name="**/resources/*" />
-            <include name="**/templates/*" />
-        </fileset>
-        <fileset dir="${java.private.source.dir}" erroronmissingdir="false">
-            <include name="**/resources/*" if="include.private" />
-            <include name="**/templates/*" if="include.private" />
-        </fileset>
-        <fileset dir="${java.protected.source.dir}" erroronmissingdir="false">
-            <include name="**/resources/*" if="include.protected" />
-            <include name="**/templates/*" if="include.protected" />
-        </fileset>
-    </path>
-
-    <!-- ******************************************************************************** -->
-    <!-- Ivy Retrieve                                                                     -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.resolve" unless="init.resolve.done">
-        <!-- ivy properties -->
-        <property name="ivy.install.version" value="2.2.0"/>
-        <property name="ivy.home" value="${user.home}/.ant"/>
-        <property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
-        <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
-        <property name="ivy.settings.dir" value="settings"/>
-        <property file="${ivy.settings.dir}/ivysettings.properties"/>
-        <property name="maven-ant-tasks.install.version" value="2.1.3"/>
-        <property name="maven-ant-tasks.jar.file" value="maven-ant-tasks-${maven-ant-tasks.install.version}.jar"/>
-
-        <mkdir dir="${lib.dir}"/>
-        <mkdir dir="${ivy.jar.dir}"/>
-
-        <!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
-
-        <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
-             dest="${ivy.jar.dir}/${ivy.jar.file}"
-             usetimestamp="true"/>
-        <taskdef resource="org/apache/ivy/ant/antlib.xml"
-                 uri="antlib:org.apache.ivy.ant"
-                 classpath="${ivy.jar.dir}/${ivy.jar.file}"/>
-
-        <get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}"
-             dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"
-             usetimestamp="true"/>
-        <taskdef resource="org/apache/maven/artifact/ant/antlib.xml"
-                 uri="antlib:antlib:org.apache.maven.artifact.ant"
-                 classpath="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"/>
-
-        <!-- End network lines -->
-
-        <ivy:settings file="${ivy.settings.dir}/ivysettings.xml"/>
-        <property name="init.resolve.done" value="true"/>
-    </target>
-
-    <target name="resolve" depends="init.resolve,init" description="Locate and download library dependencies">
-        <property name="ivy.conf" value="default"/>
-        <ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
-        <!-- Remove old versions of ivy jars AFTER the ivy:retrieve has been class loaded. -->
-        <delete file="${ivy.jar.dir}/ivy-2.0.0.jar"/>
-        <delete file="${ivy.jar.dir}/ivy-2.2.0-rc1.jar"/>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Initialization                                                                   -->
-    <!-- ******************************************************************************** -->
-
-    <!-- Targets for generating the build version -->
-    <target name="git.describe">
-      <exec executable="git" outputproperty="git.describe.output" resultproperty="git.describe.exit.value" failonerror="false">
-        <arg line="describe --long" />
-      </exec>
-      <condition property="git.describe.succeeded">
-        <equals arg1="${git.describe.exit.value}" arg2="0" />
-      </condition>
-    </target>
-
-    <target name="tagged.build.version" depends="git.describe" if="git.describe.succeeded">
-        <property name="build.version" value="${git.describe.output}" />
-    </target>
-
-    <target name="git.rev-parse" depends="git.describe" unless="git.describe.succeeded">
-      <exec executable="git" outputproperty="git.rev-parse.output" resultproperty="git.rev-parse.exit.value" failonerror="false">
-        <arg line="rev-parse --short HEAD" />
-      </exec>
-      <condition property="git.rev-parse.succeeded">
-        <equals arg1="${git.rev-parse.exit.value}" arg2="0" />
-      </condition>
-    </target>
-
-    <target name="untagged.build.version" depends="git.rev-parse" if="git.rev-parse.succeeded">
-        <property name="build.version" value="${git.rev-parse.output}" />
-    </target>
-
-    <target name="generate.build.version" depends="tagged.build.version, untagged.build.version">
-        <!-- Set build.version to exported if no other value has been set -->
-        <property name="build.version" value="exported" />
-    </target>
-
-
-    <!-- INIT OVERRIDES: call these targets BEFORE init to override build defaults -->
-    <target name="init.build.publiconly">
-        <property name="build.target" value="public" />
-    </target>
-
-    <target name="init.build.publicprotectedonly">
-        <property name="build.target" value="protected" />
-    </target>
-
-    <target name="init.build.all">
-        <property name="build.target" value="all" />
-    </target>
-
-    <target name="init.javaonly">
-        <property name="compile.scala" value="false" />
-    </target>
-
-    <target name="init.javaandscala">
-        <property name="compile.scala" value="true" />
-    </target>
-
-    <target name="init.usecontracts">
-        <property name="use.contracts" value="true" />
-    </target>
-
-
-    <!-- INIT -->
-    <target name="init" depends="generate.build.version">
-        <tstamp>
-            <format property="build.timestamp" pattern="yyyy/MM/dd HH:mm:ss"/>
-        </tstamp>
-
-        <!-- These properties should be overridden before init is called if the defaults are not desired -->
-        <property name="build.target" value="${default.build.target}" />
-        <property name="compile.scala" value="${compile.scala.by.default}" />
-        <property name="use.contracts" value="${use.contracts.by.default}" />
-        <property name="executable" value="${default.executable}" />
-
-        <!-- Determine what should be built -->
-        <condition property="include.scala">
-            <equals arg1="${compile.scala}" arg2="true" />
-        </condition>
-
-        <condition property="include.private">
-            <and>
-                <available file="${private.dir}" />
-                <equals arg1="${build.target}" arg2="all" />
-            </and>
-        </condition>
-
-        <condition property="include.protected">
-            <and>
-                <available file="${protected.dir}" />
-                <or>
-                    <equals arg1="${build.target}" arg2="all" />
-                    <equals arg1="${build.target}" arg2="protected" />
-                </or>
-            </and>
-        </condition>
-
-        <condition property="include.contracts">
-            <equals arg1="${use.contracts}" arg2="true" />
-        </condition>
-
-        <condition property="include.external">
-            <available file="${external.dir}"/>
-        </condition>
-
-        <!-- Construct display strings for the build properties print out -->
-
-        <condition property="include.scala.display.string" value="yes" else="no">
-            <isset property="include.scala" />
-        </condition>
-
-        <condition property="include.private.display.string" value="yes" else="no">
-            <isset property="include.private" />
-        </condition>
-
-        <condition property="include.protected.display.string" value="yes" else="no">
-            <isset property="include.protected" />
-        </condition>
-
-        <condition property="include.external.display.string" value="yes" else="no">
-            <isset property="include.external" />
-        </condition>
-
-        <condition property="include.contracts.display.string" value="yes" else="no">
-            <isset property="include.contracts" />
-        </condition>
-
-        <!-- Print out build properties -->
-        <echo message="BUILD PROPERTIES" />
-        <echo message="Include Scala?     : ${include.scala.display.string}" />
-        <echo message="Include Private?   : ${include.private.display.string}" />
-        <echo message="Include Protected? : ${include.protected.display.string}" />
-        <echo message="Include External?  : ${include.external.display.string}" />
-        <echo message="Include Contracts? : ${include.contracts.display.string}" />
-        <echo message="Source revision    : ${build.version}" />
-        <echo message="Build time         : ${build.timestamp}" />
-
-        <!-- Create the build directory structure used by compile -->
-        <mkdir dir="${build.dir}"/>
-        <mkdir dir="${lib.dir}"/>
-        <mkdir dir="${java.classes}"/>
-        <mkdir dir="${java.contracts.dir}"/>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Java Compilation                                                                 -->
-    <!-- ******************************************************************************** -->
-
-    <target name="gatk.compile.internal.source" depends="init,resolve">
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
-            <src refid="java.source.path" />
-            <compilerarg value="-proc:none" />
-        </javac>
-    </target>
-
-    <target name="gatk.compile.external.source" depends="gatk.compile.internal.source" if="include.external">
-        <subant target="compile" genericantfile="build.xml">
-            <property name="build.dir" refid="external.build.dir" />
-            <property name="dist.dir" refid="external.dist.dir" />
-            <property name="gatk.classpath" refid="external.gatk.classpath" />
-            <fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
-        </subant>
-    </target>
-
-    <target name="gatk.compile.source" depends="gatk.compile.internal.source,gatk.compile.external.source" />
-
-    <target name="gatk.contracts" depends="gatk.compile.source" if="include.contracts">
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.contracts.dir}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
-            <src refid="java.source.path" />
-            <classpath>
-                <path refid="external.dependencies" />
-                <pathelement path="${java.classes}" />
-            </classpath>
-            <compilerarg value="-Acom.google.java.contract.debug"/>
-            <compilerarg value="-Acom.google.java.contract.dump=${contract.dump.dir}"/>
-            <compilerarg value="-proc:only"/>
-        </javac>
-    </target>
-
-    <target name="gatk.compile" depends="init,resolve,gatk.compile.source,gatk.contracts" />
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Scala Compilation                                                                -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.queue-extensions.generate" depends="gatk.compile">
-        <condition property="uptodate.queue-extensions.generate">
-            <or>
-                <not>
-                    <isset property="include.scala"/>
-                </not>
-                <uptodate targetfile="${queue-extensions.source.dir}">
-                    <srcfiles refid="java.class.files"/>
-                    <srcfiles file="${queue-extensions.gatk.jar}"/>
-                </uptodate>
-            </or>
-        </condition>
-    </target>
-
-    <!-- NOTE: Extracting help first to avoid "Unable to load help text.  Help output will be sparse." warning message. -->
-    <target name="queue-extensions.generate" depends="gatk.compile,extracthelp,init.queue-extensions.generate" unless="uptodate.queue-extensions.generate">
-        <mkdir dir="${queue-extensions.source.dir}"/>
-        <echo>Generating Queue GATK extensions...</echo>
-        <java fork="true" failonerror="true" classname="org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator" >
-            <arg value="-outDir" />
-            <arg path="${queue-extensions.source.dir}" />
-            <arg value="-l" />
-            <arg value="WARN" />
-            <classpath>
-                <file file="${queue-extensions.gatk.jar}"/>
-                <path refid="scala.dependencies"/>
-            </classpath>
-        </java>
-        <touch>
-            <file file="${queue-extensions.source.dir}"/>
-        </touch>
-    </target>
-
-    <target name="init.scala.compile" depends="resolve">
-        <path id="scala.classpath">
-            <fileset dir="${lib.dir}">
-                <include name="scala-compiler-*.jar"/>
-                <include name="scala-library-*.jar"/>
-                <include name="scala-reflect-*.jar"/>
-            </fileset>
-        </path>
-        <taskdef resource="scala/tools/ant/antlib.xml">
-            <classpath refid="scala.classpath"/>
-        </taskdef>
-    </target>
-
-    <!-- Scala depends on the java compile -->
-    <target name="scala.compile" depends="init,resolve,gatk.compile,queue-extensions.generate,init.scala.compile" if="include.scala">
-        <mkdir dir="${scala.classes}"/>
-        <echo>Building Scala...</echo>
-        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes" addparams="-feature">
-            <src refid="scala.source.path" />
-            <src path="${queue-extensions.source.dir}" />
-            <include name="**/*.scala" />
-        </scalac>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Sting Resource File Generation                                                   -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.extracthelp" depends="gatk.compile">
-        <loadfile property="properties.version" srcfile="${basedir}/${resource.path}" failonerror="false" quiet="true">
-            <filterchain>
-                <linecontains>
-                    <contains value="org.broadinstitute.sting.gatk.CommandLineGATK.version"/>
-                </linecontains>
-                <tokenfilter>
-                    <replaceregex pattern="^.*\.(.*?)$" replace="\1"/>
-                </tokenfilter>
-                <striplinebreaks/>
-            </filterchain>
-        </loadfile>
-
-        <!-- This fileset will contain only source files modified since the resource file was last generated,
-             or all source files if the resource file doesn't exist -->
-        <fileset dir="${basedir}" id="modified.source.files">
-            <patternset refid="java.source.files.pattern" />
-            <include name="${external.dir}/**/*.java"/>
-            <depend targetdir="${basedir}">
-                <mapper type="merge" to="${resource.path}"/>
-            </depend>
-        </fileset>
-
-        <!-- Set the sources.modified property only if our fileset of modified source files is non-empty -->
-        <pathconvert refid="modified.source.files" property="sources.modified" setonempty="false"/>
-
-        <!-- Due to a limitation in the doclet API, we always need to pass package-info files to javadoc -->
-        <fileset dir="${basedir}" id="package.info.files">
-            <include name="${java.public.source.dir}/**/package-info.java"/>
-            <include name="${java.private.source.dir}/**/package-info.java" if="include.private" />
-            <include name="${java.protected.source.dir}/**/package-info.java" if="include.protected" />
-            <include name="${external.dir}/**/package-info.java"/>
-        </fileset>
-
-        <condition property="uptodate.extracthelp">
-            <or>
-                <isset property="disable.help"/>
-                <and>
-                    <not>
-                        <isset property="sources.modified"/>
-                    </not>
-                    <equals arg1="${properties.version}" arg2="${build.version}"/>
-                </and>
-            </or>
-        </condition>
-    </target>
-
-    <target name="extracthelp" depends="init.extracthelp" unless="uptodate.extracthelp">
-        <path id="doclet.classpath">
-            <path refid="external.dependencies" />
-            <pathelement location="${java.classes}" />
-	    <pathelement location="${clover.jar}" />
-        </path>
-
-        <javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
-                 docletpathref="doclet.classpath"
-                 classpathref="external.dependencies"
-                 classpath="${java.classes}"
-		 maxmemory="2g"
-                 additionalparam="-build-timestamp &quot;${build.timestamp}&quot; -absolute-version ${build.version} -out ${basedir}/${resource.path} -quiet">
-            <sourcefiles>
-                <union>
-                    <fileset refid="modified.source.files"/>
-                    <fileset refid="package.info.files"/>
-                </union>
-            </sourcefiles>
-        </javadoc>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Build Jars                                                                       -->
-    <!-- ******************************************************************************** -->
-
-    <target name="sting.compile" depends="gatk.compile, scala.compile" />
-
-    <target name="init.jar" depends="sting.compile,extracthelp">
-        <mkdir dir="${dist.dir}"/>
-        <copy todir="${dist.dir}">
-            <fileset dir="${lib.dir}" includes="*.jar"/>
-        </copy>
-    </target>
-
-    <target name="R.public.tar">
-        <mkdir dir="${R.tar.dir}/${R.package.path}" />
-        <tar compression="gzip" basedir="${R.public.src.dir}/${R.package.path}" includes="gsalib/**" destfile="${R.tar.dir}/${R.package.path}/gsalib.tar.gz" />
-    </target>
-
-    <target name="R.script.stage">
-        <mkdir dir="${R.script.staging.dir}" />
-        <copy todir="${R.script.staging.dir}" overwrite="true">
-            <fileset refid="R.script.source.files" />
-            <!-- remove the initial path components (eg., public/R/scripts) when doing the copy -->
-            <!-- ant 1.8.2 has a cutdirsmapper, but ant versions < 1.8.2 are too common to use it -->
-            <mapper type="regexp" from="^(${R.public.scripts.dir}|${R.private.scripts.dir}|${R.protected.scripts.dir})/(.*)" to="\2" />
-        </copy>
-    </target>
-
-    <target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
-        <jar jarfile="${dist.dir}/StingUtils.jar">
-            <fileset dir="${java.classes}" includes="**/sting/utils/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
-            <fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
-            <fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/>
-            <fileset dir="${R.tar.dir}">
-                <include name="**/${R.package.path}/**/*.tar.gz"/>
-            </fileset>
-            <fileset dir="${R.script.staging.dir}">
-                <include name="**/sting/utils/**/*.R"/>
-            </fileset>
-            <manifest>
-                <attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="na12878kb.jar" depends="gatk.compile,init.jar">
-        <jar jarfile="${dist.dir}/na12878kb.jar">
-            <fileset dir="${java.classes}">
-              <include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
-              <include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
-              <include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
-              <include name="org/broadinstitute/sting/utils/BaseUtils*.class"/>
-              <include name="org/broadinstitute/sting/utils/Utils.class"/>
-              <include name="org/broadinstitute/sting/utils/MRUCaching*.class"/>
-              <include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
-              <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
-              <include name="net/sf/picard/reference/FastaSequenceFile.class"/>
-            </fileset>
-	    <fileset dir="${java.private.source.dir}">
-              <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/resources/**/*"/>
-	    </fileset>
-        </jar>
-    </target>
-
-    <target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage">
-        <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
-            <path refid="gatk.resources"/>
-            <fileset dir="${java.contracts.dir}" />
-            <fileset dir="${java.classes}">
-	          <include name="${resource.file}" />
-              <include name="**/sting/gatk/**/*.class" />
-              <include name="**/sting/alignment/**/*.class"/>
-            </fileset>
-            <fileset dir="${R.script.staging.dir}">
-                <include name="**/sting/gatk/**/*.R"/>
-                <include name="**/sting/alignment/**/*.R"/>
-            </fileset>
-            <fileset dir="${key.dir}">
-                <include name="**/*.key"/>
-            </fileset>
-            <manifest>
-                <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK" />
-            </manifest>
-        </jar>
-
-        <jar jarfile="${dist.dir}/Aligner.jar">
-            <fileset dir="${java.classes}" includes="**/sting/alignment/**/*.class" />
-        </jar>
-
-        <subant target="dist" genericantfile="build.xml">
-            <property name="build.dir" refid="external.build.dir" />
-            <property name="dist.dir" refid="external.dist.dir" />
-            <property name="gatk.classpath" refid="external.gatk.classpath" />
-            <fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
-        </subant>
-    </target>
-
-    <target name="scala.jar" depends="scala.compile, init.jar" if="include.scala">
-        <jar jarfile="${dist.dir}/GATKScala.jar">
-          <fileset dir="${scala.classes}">
-            <include name="org/broadinstitute/sting/scala/**/*.class"/>
-          </fileset>
-        </jar>
-    </target>
-
-    <target name="queue.jar" depends="scala.compile, init.jar, R.script.stage" if="include.scala">
-        <jar jarfile="${dist.dir}/Queue.jar">
-            <fileset dir="${scala.classes}">
-                <include name="org/broadinstitute/sting/queue/**/*.class"/>
-            </fileset>
-            <fileset dir="${java.classes}">
-              <include name="org/broadinstitute/sting/queue/**/*.class" />
-            </fileset>
-            <fileset dir="${R.script.staging.dir}">
-                <include name="org/broadinstitute/sting/queue/**/*.R"/>
-            </fileset>
-            <manifest>
-                <attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="sting.jar" depends="sting-utils.jar, gatk.jar, queue.jar" />
-
-    <target name="init.manifests" depends="sting.jar">
-        <pathconvert property="jar.classpath" pathsep=" ">
-            <flattenmapper/>
-            <fileset dir="${dist.dir}" includes="*.jar"/>
-            <filelist files="GATKScala.jar"/>
-        </pathconvert>
-    </target>
-
-    <target name="sting-utils.manifests" depends="sting-utils.jar, init.manifests">
-        <jar jarfile="${dist.dir}/StingUtils.jar" update="true">
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}"/>
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="gatk.manifests" depends="gatk.jar, init.manifests">
-        <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar" update="true">
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}"/>
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="queue.manifests" depends="queue.jar, init.manifests" if="include.scala">
-        <jar jarfile="${dist.dir}/Queue.jar" update="true" >
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}" />
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="sting.manifests" depends="sting-utils.manifests, gatk.manifests, queue.manifests" />
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Top-Level Build Targets                                                          -->
-    <!-- ******************************************************************************** -->
-
-    <target name="dist" depends="sting.manifests" description="Build the GATK and Queue" />
-
-    <target name="gatk" depends="init.javaonly, sting.manifests" description="Build the GATK only" />
-
-    <target name="queue" depends="dist" />  <!-- Obsolete target. Now just an alias for dist -->
-
-    <target name="scala" depends="scala.jar" />
-
-
-    <!-- ******************************************************************************** -->
-    <!-- GATKDocs                                                                          -->
-    <!-- ******************************************************************************** -->
-
-    <target name="gatkdocs" depends="gatk.compile" description="Generate GATK HTML documentation">
-        <path id="doclet.classpath">
-            <path refid="external.dependencies" />
-            <pathelement location="${java.classes}" />
-        </path>
-
-        <!-- Run with -Dgatkdocs.include.hidden=true to include documentation for hidden features -->
-        <condition property="gatkdocs.include.hidden.arg" value="-include-hidden" else="">
-            <isset property="gatkdocs.include.hidden" />
-        </condition>
-
-        <javadoc doclet="org.broadinstitute.sting.utils.help.GATKDoclet"
-                 docletpathref="doclet.classpath"
-                 classpathref="external.dependencies"
-                 classpath="${java.classes}"
-		 maxmemory="2g"
-                 additionalparam="${gatkdocs.include.hidden.arg} -private -build-timestamp &quot;${build.timestamp}&quot; -absolute-version ${build.version} -quiet"> <!-- -test to only do DocumentationTest walker -->
-            <sourcefiles>
-                <fileset refid="java.source.files"/>
-            </sourcefiles>
-        </javadoc>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Javadoc                                                                          -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.javadoc">
-        <mkdir dir="${javadoc.dir}" />
-    </target>
-
-    <target name="javadoc" depends="init.javadoc,resolve" description="Generate Javadoc">
-        <javadoc destdir="${javadoc.dir}" classpathref="external.dependencies">
-            <fileset refid="java.source.files" />
-            <sourcepath path="${external.dir}" />
-        </javadoc>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Scaladoc                                                                         -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.scaladoc">
-        <mkdir dir="${scaladoc.dir}" />
-    </target>
-
-    <!-- NOTE: the scaladoc target requires that the environment variable ANT_OPTS has been set to "-Xmx1G" -->
-
-    <target name="scaladoc" depends="resolve,queue-extensions.generate,init.scala.compile,scala.compile,init.scaladoc" description="Generate Scaladoc">
-        <scaladoc srcdir="${basedir}" destdir="${scaladoc.dir}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
-            <patternset refid="scala.source.files.pattern" />
-            <include name="${queue-extensions.source.dir}/**/*.scala" />
-        </scaladoc>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Release-related tasks                                                            -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.executable.gatkfull" depends="init.build.publicprotectedonly, init.javaonly">
-        <property name="executable" value="GenomeAnalysisTK" />
-    </target>
-
-    <target name="init.executable.gatkall" depends="init.build.all, init.javaonly">
-        <property name="executable" value="GenomeAnalysisTK" />
-    </target>
-
-    <target name="init.executable.queuefull" depends="init.build.publicprotectedonly, init.javaandscala">
-        <property name="executable" value="Queue" />
-    </target>
-
-    <target name="init.executable.queueall" depends="init.build.all, init.javaandscala">
-        <property name="executable" value="Queue" />
-    </target>
-
-    <target name="require.executable">
-        <condition property="no.executable.defined">
-            <or>
-                <equals arg1="${executable}" arg2="none" />
-                <equals arg1="${executable}" arg2="$${executable}" />
-            </or>
-        </condition>
-        <fail message="No executable defined. Call a more specific packaging/release target, or define an executable manually" if="no.executable.defined" />
-    </target>
-
-    <target name="require.bcel">
-        <fileset id="bcel.jar" dir="${user.home}/.ant/lib">
-            <include name="bcel-*.jar" />
-        </fileset>
-        <pathconvert refid="bcel.jar" property="bcel.jar.installed" setonempty="false" />
-
-        <fileset id="ant.bcel.jar" dir="${user.home}/.ant/lib">
-            <include name="ant-apache-bcel-*.jar" />
-        </fileset>
-        <pathconvert refid="ant.bcel.jar" property="ant.bcel.jar.installed" setonempty="false" />
-
-        <condition property="bcel.installed">
-            <and>
-                <isset property="bcel.jar.installed" />
-                <isset property="ant.bcel.jar.installed" />
-            </and>
-        </condition>
-        <fail unless="bcel.installed"
-              message="Required bcel libraries for GATK packaging not installed in ${user.home}/.ant/lib/${line.separator}The bcel jar can be found in the lib directory of a GATK clone after compiling, and the ant-apache-bcel jar can be downloaded from here: http://repo1.maven.org/maven2/ant/ant-apache-bcel/1.6.5/ant-apache-bcel-1.6.5.jar${line.separator}Please copy these two jar files to ${user.home}/.ant/lib/" />
-    </target>
-
-    <!-- Unzip all classes from their current locations and assemble them in a staging directory -->
-    <target name="stage">
-        <mkdir dir="${staging.dir}"/>
-        <!--
-            HACK: Create the edu directory before EDU on case-insensitive mac filesystems.
-            The ivy dependency colt -> concurrent contains an EDU.oswego package which
-            BCEL doesn't even pull in but messes up edu.mit.broad.
-          -->
-        <mkdir dir="${staging.dir}/edu"/>
-        <unjar dest="${staging.dir}" overwrite="false">
-          <fileset dir="${dist.dir}">
-            <patternset refid="dependency.mask" />
-          </fileset>
-        </unjar>
-
-        <!-- HACK: The GATK jar itself contains overrides for some core classes.  Make sure the GATK.jar is unrolled last. -->
-        <unjar dest="${staging.dir}" overwrite="true">
-          <fileset dir="${dist.dir}" includes="**/GenomeAnalysisTK.jar"/>
-        </unjar>
-    </target>
-
-
-    <!-- Build a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
-    <target name="package" depends="require.clean,require.bcel,dist,stage,require.executable">
-      <mkdir dir="${package.output.dir}" />
-      <xslt destdir="${package.output.dir}" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
-          <flattenmapper/>
-          <fileset dir="${package.xml.dir}">
-              <include name="${executable}.xml" />
-          </fileset>
-          <fileset dir="${external.dir}" erroronmissingdir="false">
-              <include name="*/${executable}.xml" />
-          </fileset>
-      </xslt>
-      <ant antfile="${package.output.dir}/${executable}.xml" target="package" />
-    </target>
-
-    <!-- Package specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
-
-    <!-- GATK "full" == public + protected, ie., the standard binary release of the GATK  -->
-    <target name="package.gatk.full" depends="init.executable.gatkfull,package" description="Create a standalone GATK jar with public and protected code" />
-
-    <!-- GATK "all" == public + protected + private. Should never be publicly released -->
-    <target name="package.gatk.all" depends="init.executable.gatkall,package" description="Create a standalone GATK jar with public, protected, and private code" />
-
-    <target name="package.queue.full" depends="init.executable.queuefull,package" description="Create a standalone Queue jar with public and protected code" />
-
-    <target name="package.queue.all" depends="init.executable.queueall,package" description="Create a standalone Queue jar with public, protected, and private code" />
-
-    <!-- Release a build. Don't call this target directly. Call one of the specific release targets below -->
-    <target name="release" depends="require.executable">
-        <ant antfile="${package.output.dir}/${executable}.xml" target="release" />
-    </target>
-
-    <!-- Release specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
-    <target name="release.gatk.full" depends="package.gatk.full,release" />
-
-    <target name="release.queue.full" depends="package.queue.full,release" />
-
-    <!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
-    <!-- TODO: Reuse as much as possible of the 'stage' and 'package' targets -->
-    <target name="build-picard-private" depends="resolve">
-      <!-- Build out a classpath -->
-      <pathconvert property="required.picard.jars" pathsep=":">
-        <fileset dir="${basedir}">
-	     <include name="${staging.dir}" />
-	     <include name="${lib.dir}/picard-*.*.*.jar" />
-	     <include name="${lib.dir}/sam-*.jar" />
-	   </fileset>
-      </pathconvert>
-      <echo message="required.picard.jars=${required.picard.jars}" />
-
-      <!-- Stage picard-private -->
-      <delete dir="${staging.dir}" />
-      <mkdir dir="${staging.dir}" />
-      <unjar src="${picard.dist.dir}/picard-private.jar" dest="${staging.dir}" overwrite="true" />
-
-      <!-- Use the packaging system to extract parts of picard-private we need -->
-      <mkdir dir="${package.output.dir}" />
-      <xslt in="${package.xml.dir}/PicardPrivate.xml" out="${package.output.dir}/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
-      <ant antfile="${package.output.dir}/BuildPicardPrivate.xml">
-	    <property name="additional.jars" value="${required.picard.jars}" />
-      </ant>
-    </target>
-
-    <!-- Maven install a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
-    <target name="mvninstall" depends="package">
-        <property name="mvn.build.version" value="0.0.2" />
-        <!--
-        We should use the build version or better yet a git tag version, but tags are currently missing. Alternatively how do we then depend on the LATEST?
-        <property name="mvn.build.version" value="${build.version}" />
-        -->
-        <artifact:pom id="${executable}.pom" groupId="org.broadinstitute.sting" artifactId="${executable}" version="${mvn.build.version}" name="${executable}" />
-        <artifact:writepom pomRefId="${executable}.pom" file="${package.output.dir}/${executable}-${build.version}/${executable}.pom.xml"/>
-        <artifact:install file="${package.output.dir}/${executable}-${build.version}/${executable}.jar">
-            <artifact:pom file="${package.output.dir}/${executable}-${build.version}/${executable}.pom.xml" />
-        </artifact:install>
-    </target>
-
-    <!-- Maven install specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
-    <target name="mvninstall.gatk.full" depends="package.gatk.full,mvninstall" />
-
-    <target name="mvninstall.queue.all" depends="package.queue.all,mvninstall" />
-
-    <target name="mvninstall.queue.full" depends="package.queue.full,mvninstall" />
-
-    <!-- ******************************************************************************** -->
-    <!-- Clean                                                                            -->
-    <!-- ******************************************************************************** -->
-
-    <target name="clean.gatkdocs">
-        <delete dir="${gatkdocs.dir}"/>
-    </target>
-
-    <target name="clean.javadoc">
-        <delete dir="${javadoc.dir}" />
-    </target>
-
-    <target name="clean.scaladoc">
-        <delete dir="${scaladoc.dir}" />
-    </target>
-
-    <target name="-check.clover">
-      <available property="clover.installed" classname="com.cenqua.clover.CloverInstr" />
-    </target>
-
-    <target name="clean.clover" depends="-check.clover" if="clover.installed">
-      <clover-clean/>
-    </target>
-
-    <target name="clean.gsalib">
-        <!-- Currently not cleaning out the lib during 'ant clean' -->
-      <exec executable="R" failonerror="false">
-        <arg line="R CMD REMOVE gsalib" />
-      </exec>
-    </target>
-
-    <target name="clean" description="Clean up old build-related directories" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs,clean.clover">
-        <delete dir="${build.dir}"/>
-        <delete dir="${lib.dir}"/>
-        <delete dir="${contract.dump.dir}"/>
-        <delete dir="${staging.dir}"/>
-        <delete dir="${dist.dir}"/>
-        <delete dir="${pipelinetest.dir}"/>
-        <delete dir="${integration.tests.dir}"/>
-    </target>
-
-    <!-- Depend on this target if your target requires a clean working directory but you don't want to depend on clean directly -->
-    <target name="require.clean">
-        <condition property="not.clean">
-            <or>
-                <available file="${build.dir}" />
-                <available file="${lib.dir}" />
-                <available file="${contract.dump.dir}" />
-                <available file="${staging.dir}" />
-                <available file="${dist.dir}" />
-                <available file="${pipelinetest.dir}" />
-                <available file="${integration.tests.dir}" />
-                <available file="${javadoc.dir}" />
-                <available file="${scaladoc.dir}" />
-                <available file="${gatkdocs.dir}" />
-            </or>
-        </condition>
-        <fail message="Selected build target requires a clean working directory. Run ant clean and then try again." if="not.clean" />
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- gsalib                                                                           -->
-    <!-- ******************************************************************************** -->
-
-    <!-- Build gsalib R module -->
-    <target name="gsalib" description="Build the gsalib R module">
-      <exec executable="R" failonerror="true">
-        <arg line="R CMD INSTALL --preclean ${R.public.src.dir}/${R.package.path}/gsalib" />
-      </exec>
-    </target>
-
-
-    <!-- ***************************************************************************** -->
-    <!-- ***********               Tests and associated tasks                ********* -->
-    <!-- ***************************************************************************** -->
-
-    <!-- Properties and Paths -->
-
-    <property name="java.test.classes" value="${build.dir}/java/testclasses"/>
-    <property name="java.public.test.sources" value="${public.dir}/java/test"/>
-    <property name="java.private.test.sources" value="${private.dir}/java/test"/>
-    <property name="java.protected.test.sources" value="${protected.dir}/java/test"/>
-    <property name="scala.test.classes" value="${build.dir}/scala/testclasses"/>
-    <property name="scala.public.test.sources" value="${public.dir}/scala/test"/>
-    <property name="scala.private.test.sources" value="${private.dir}/scala/test"/>
-    <property name="scala.protected.test.sources" value="${protected.dir}/scala/test"/>
-    <property name="integration.tests.dir" value="integrationtests" />
-    <property name="pipelinetest.dir" value="pipelinetests" />
-    <property name="report" value="${build.dir}/report"/>
-    <property name="iwww.report.dir" value="${user.home}/private_html/report"/>
-    <property name="test.output" value="${dist.dir}/test"/>
-    <property name="testng.jar" value="${lib.dir}/testng-6.8.jar"/>
-
-    <path id="java.test.source.path">
-        <dirset dir="${basedir}">
-            <include name="${java.public.test.sources}" />
-            <include name="${java.private.test.sources}" if="include.private" />
-            <include name="${java.protected.test.sources}" if="include.protected" />
-        </dirset>
-    </path>
-
-    <path id="scala.test.source.path">
-        <dirset dir="${basedir}">
-            <include name="${scala.public.test.sources}" />
-            <include name="${scala.private.test.sources}" if="include.private" />
-            <include name="${scala.protected.test.sources}" if="include.protected" />
-        </dirset>
-    </path>
-
-    <path id="testng.dependencies">
-        <fileset dir="${lib.dir}">
-            <include name="jcommander*.jar"/>
-            <include name="guice*.jar"/>
-            <include name="junit*.jar"/>
-            <include name="bsh*.jar"/>
-            <include name="snakeyaml*.jar"/>
-            <include name="reportng*.jar"/>
-        </fileset>
-    </path>
-
-    <path id="testng.default.classpath">
-        <path refid="build.results" />
-        <pathelement path="${clover.jar}"/>
-        <pathelement location="${java.contracts.dir}" />
-        <pathelement location="${java.test.classes}" />
-        <pathelement location="${scala.test.classes}" />
-    </path>
-
-    <!-- Test targets -->
-
-    <target name="clover.report">
-      <clover-report coverageCacheSize="nocache">
-      <current outfile="clover_html" title="GATK clover report" showUniqueCoverage="false" numThreads="4">
-	  <format type="html" filter="catch,static,property"/>
-	  <fileset dir="public">
-	    <patternset id="clover.excludes">
-	      <exclude name="**/*UnitTest.java"/>
-	      <exclude name="**/*TestProvider*.java"/>
-	      <exclude name="**/*PerformanceTest.java"/>
-	      <exclude name="**/*Benchmark.java"/>
-	      <exclude name="**/*LargeScaleTest.java"/>
-	      <exclude name="**/*IntegrationTest.java"/>
-	      <exclude name="**/jna/**/*.java"/>
-	      <exclude name="**/queue/extensions/**/*.java"/>
-	      <exclude name="**/sting/utils/help/*.java"/>
-	      <exclude name="**/sting/tools/*.java"/>
-	      <exclude name="**/datasources/reads/utilities/*.java"/>
-	      <exclude name="**/sting/alignment/**/*.java"/>
-	      <exclude name="**/examples/**/*.java"/>
-	    </patternset>
-	  </fileset>
-	  <fileset dir="private">
-	    <patternset refid="clover.excludes" />
-	  </fileset>
-	  <fileset dir="protected">
-	    <patternset refid="clover.excludes" />
-	  </fileset>
-	</current>
-      </clover-report>
-    </target>
-
-    <target name="with.clover">
-      <clover-setup fullyQualifyJavaLang="true" instrumentationLevel="${clover.instrument.level}">
-      </clover-setup>
-      <property name="compile.scala" value="false" /> <!-- currently doesn't work with scala -->
-      <property name="test.maxmemory" value="32g"/>  <!-- clover requires lots of memory -->
-      <echo message="Clover instrument level: ${clover.instrument.level}" />
-    </target>
-
-    <target name="test.init.compile">
-        <mkdir dir="${java.test.classes}"/>
-        <mkdir dir="${scala.test.classes}"/>
-    </target>
-
-   <target name="test.java.internal.compile" depends="dist,test.init.compile">
-        <echo message="Sting: Compiling java test cases!"/>
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
-            <src refid="java.test.source.path" />
-            <classpath>
-                <path refid="build.results" />
-                <pathelement location="${java.contracts.dir}"/>
-            </classpath>
-            <compilerarg value="-proc:none"/>
-        </javac>
-    </target>
-
-    <target name="test.java.external.compile" depends="dist,test.init.compile,test.java.internal.compile" if="include.external">
-        <echo message="Sting: Compiling external java test cases!"/>
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}" srcdir="${external.dir}">
-            <include name="*/test/**/*.java"/>
-            <classpath>
-                <path refid="build.results" />
-                <pathelement location="${java.test.classes}"/>
-                <pathelement location="${java.contracts.dir}"/>
-            </classpath>
-            <compilerarg value="-proc:none"/>
-        </javac>
-    </target>
-
-    <target name="test.java.compile" depends="test.java.internal.compile, test.java.external.compile"/>
-
-    <target name="test.scala.compile" depends="test.java.compile,scala.compile" if="include.scala">
-        <echo message="Scala: Compiling test cases!"/>
-        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes" addparams="-feature">
-	        <src refid="scala.test.source.path" />
-            <classpath>
-                <path refid="build.results"/>
-                <pathelement location="${java.test.classes}"/>
-            </classpath>
-        </scalac>
-    </target>
-
-    <!-- NOTE: contracts disabled for all tests now, since contracts don't work with Java 7 -->
-    <target name="test.compile" depends="dist,test.java.compile,test.scala.compile" />
-
-
-    <!-- Run test macro -->
-    <macrodef name="run-test">
-        <attribute name="testtype"/>
-        <attribute name="outputdir"/>
-        <attribute name="runfailed"/>
-
-        <sequential>
-            <condition property="run.failed.tests">
-                <equals arg1="@{runfailed}" arg2="true"/>
-            </condition>
-
-            <!-- Get the pipeline run type.  Default to dry.  -->
-            <condition property="pipeline.run" value="dry" else="${pipeline.run}">
-                <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
-            </condition>
-
-            <condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
-                <isset property="include.contracts" />
-            </condition>
-
-            <condition property="debug.jvm.args" value="-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${test.debug.port}" else="">
-                <isset property="test.debug" />
-            </condition>
-
-            <mkdir dir="@{outputdir}"/>
-
-            <echo message="" />
-            <echo message="Test Classpath ID: ${testng.classpath}" />
-            <property name="test.classpath.display.string" refid="${testng.classpath}" />
-            <echo message="Test Classpath: ${test.classpath.display.string}" />
-            <echo message="" />
-            <echo message="Sting: Running @{testtype} test cases!"/>
-            <echo message="Test Memory : ${test.maxmemory}" />
-
-	    <!-- no test is allowed to run for more than 10 hours -->
-            <taskdef resource="testngtasks" classpath="${testng.jar}"/>
-            <testng outputDir="@{outputdir}"
-                    classpathref="${testng.classpath}"
-                    haltOnFailure="false" failureProperty="test.failure"
-                    verbose="2"
-		            timeout="36000000"
-                    workingDir="${basedir}"
-                    useDefaultListeners="false"
-                    listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.TestNGTestTransformer,org.broadinstitute.sting.StingTextReporter,org.uncommons.reportng.HTMLReporter">
-                <jvmarg value="-Xmx${test.maxmemory}" />
-                <jvmarg value="-ea" />
-                <jvmarg value="-Dclover.pertest.coverage=diff" />
-                <jvmarg value="-Djava.awt.headless=true" />
-                <jvmarg value="-Dpipeline.run=${pipeline.run}" />
-                <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
-                <jvmarg line="${cofoja.jvm.args}"/>
-                <jvmarg line="${debug.jvm.args}"/>
-
-                <!-- NOTE: To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
-
-                <classfileset dir="${java.test.classes}" includes="**/@{testtype}.class"/>
-                <classfileset dir="${java.external.test.classes}" erroronmissingdir="false">
-                    <include name="**/@{testtype}.class" if="include.external"/>
-                </classfileset>
-                <classfileset dir="${scala.test.classes}" erroronmissingdir="false">
-                    <include name="**/@{testtype}*.class" if="include.scala"/>
-                </classfileset>
-
-                <xmlfileset dir="${basedir}">
-                    <include name="@{testtype}" if="run.failed.tests"/>
-                </xmlfileset>
-            </testng>
-
-            <!-- generate a report for Bamboo or Hudson to read in -->
-            <junitreport todir="@{outputdir}">
-                <fileset dir="@{outputdir}">
-                    <include name="*/*.xml"/>
-                </fileset>
-                <report format="noframes" todir="@{outputdir}"/>
-            </junitreport>
-
-	    <!-- copy the report to our private_html directory for easy viewing in a broswer -->
-            <mkdir dir="${iwww.report.dir}/@{testtype}"/>
-            <copy todir="${iwww.report.dir}/@{testtype}" verbose="false">
-              <fileset dir="@{outputdir}"/>
-            </copy>
-
-            <fail message="test failed" if="test.failure" />
-        </sequential>
-    </macrodef>
-
-
-    <target name="test.init">
-        <property name="testng.classpath" value="testng.default.classpath" />
-        <property name="test.maxmemory" value="${test.default.maxmemory}"/>
-    </target>
-
-    <target name="init.testgatkjar">
-        <path id="gatk.binary.release.tests.classpath">
-            <path refid="testng.dependencies" />
-            <path>
-                <fileset dir="${package.output.dir}">
-                    <include name="**/${executable}.jar" />
-                </fileset>
-            </path>
-            <pathelement location="${java.contracts.dir}" />
-            <pathelement location="${java.test.classes}" />
-            <pathelement location="${scala.test.classes}" />
-            <pathelement location="${scala.classes}" />
-            <path>
-                <fileset dir="${lib.dir}">
-                    <include name="scala*.jar"/>
-                    <include name="jna*.jar"/>
-                    <include name="cofoja*.jar"/>
-                </fileset>
-            </path>
-        </path>
-        <property name="testng.classpath" value="gatk.binary.release.tests.classpath" />
-    </target>
-
-    <target name="init.testqueuejar">
-        <path id="queue.binary.release.tests.classpath">
-            <path refid="testng.dependencies" />
-            <path>
-                <fileset dir="${package.output.dir}">
-                    <include name="**/${executable}.jar" />
-                </fileset>
-            </path>
-            <pathelement location="${java.contracts.dir}" />
-            <pathelement location="${java.test.classes}" />
-            <pathelement location="${scala.test.classes}" />
-            <path>
-                <fileset dir="${lib.dir}">
-                    <include name="cofoja*.jar"/>
-                </fileset>
-            </path>
-        </path>
-        <property name="testng.classpath" value="queue.binary.release.tests.classpath" />
-    </target>
-
-
-    <target name="committests" depends="unittest,integrationtest,pipelinetest" description="Run unit tests, integration tests, and do a dry-run of the pipeline tests" />
-
-    <!-- Order of the dependencies is significant in the *.release.tests targets -->
-    <target name="gatkfull.binary.release.tests" depends="package.gatk.full,init.testgatkjar,unittest,integrationtest" />
-
-    <target name="queuefull.binary.release.tests" depends="package.queue.full,init.testqueuejar,pipelinetest" />
-
-    <!-- Our four different test types: UnitTest, IntegrationTest, LargeScaleTest, PipelineTest -->
-    <target name="unittest" depends="test.compile,test.init" description="Run unit tests">
-        <condition property="ttype" value="*UnitTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${ttype}" outputdir="${report}/${ttype}" runfailed="false"/>
-    </target>
-
-    <!-- Keep the alias "test" for "unittest" for backwards compatibility -->
-    <target name="test" depends="unittest" />
-
-    <target name="integrationtest" depends="test.compile,test.init" description="Run integration tests">
-        <condition property="itype" value="*IntegrationTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${itype}" outputdir="${report}/${itype}" runfailed="false"/>
-    </target>
-
-    <target name="largescaletest" depends="test.compile,test.init" description="Run large-scale tests">
-       <condition property="ptype" value="*LargeScaleTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${ptype}" outputdir="${report}/${ptype}" runfailed="false"/>
-    </target>
-
-    <target name="pipelinetest" depends="test.compile,test.init" description="Dry-run pipeline tests">
-        <condition property="pipetype" value="*PipelineTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
-    </target>
-
-    <target name="pipelinetestrun" depends="test.compile,test.init" description="Run pipeline tests">
-        <property name="pipeline.run" value="run"/>
-        <condition property="pipetype" value="*PipelineTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
-    </target>
-
-    <target name="knowledgebasetest" depends="test.compile,test.init" description="Run knowledge base tests">
-        <condition property="ktype" value="*KnowledgeBaseTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${ktype}" outputdir="${report}/${ktype}" runfailed="false"/>
-    </target>
-
-    <target name="failed-unit" depends="test.compile,test.init">
-        <run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
-    </target>
-
-    <target name="failed-integration" depends="test.compile,test.init">
-        <run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
-    </target>
-
-    <target name="failed-largescale" depends="test.compile,test.init">
-        <run-test testtype="${report}/*LargeScaleTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
-    </target>
-
-    <target name="failed-pipeline" depends="test.compile,test.init">
-        <run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
-    </target>
-
-
-    <!-- Fast test target that cuts major corners for speed. Requires that a full build has been done first. Java-only, single test class only -->
-    <!-- Usage: ant fasttest -Dsingle=TestClass -->
-    <target name="fasttest" depends="init.javaonly,init" description="Quickly run a single test">
-	<property name="test.maxmemory" value="${test.default.maxmemory}"/>
-        <condition property="not.clean">
-            <and>
-                <available file="${build.dir}" />
-                <available file="${lib.dir}" />
-                <available file="${dist.dir}" />
-                <available file="${java.test.classes}" />
-            </and>
-        </condition>
-        <fail message="fasttest requires a NON-CLEAN working directory (INCLUDING test classes). Do a full test build using ant test.compile first." unless="not.clean" />
-
-        <condition property="no.single.test.specified">
-            <equals arg1="${single}" arg2="$${single}" />
-        </condition>
-        <fail message="Must specify a specific test. Usage: ant fasttest -Dsingle=TestClass" if="no.single.test.specified" />
-
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
-            <src refid="java.source.path" />
-            <compilerarg value="-proc:none" />
-        </javac>
-
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
-            <src refid="java.test.source.path" />
-            <classpath>
-                <pathelement location="${java.classes}"/>
-                <path refid="external.dependencies" />
-            </classpath>
-            <compilerarg value="-proc:none"/>
-        </javac>
-
-        <!-- fasttest uses the unpackaged class files in its test classpath to avoid having to rebuild the jars in dist/ -->
-        <path id="testng.fasttest.classpath">
-            <pathelement location="${java.classes}" />
-            <pathelement location="${scala.classes}" />
-            <pathelement location="${java.contracts.dir}" />
-            <pathelement location="${java.test.classes}" />
-            <pathelement location="${scala.test.classes}" />
-            <pathelement location="${R.tar.dir}" />
-            <path refid="R.script.source.path" />
-            <pathelement location="${key.dir}" />
-            <path refid="external.dependencies" />
-            <path refid="java.source.path" />  <!-- Terrible hack to allow fasttest to see resource files stored in the source tree -->
-        </path>
-        <property name="testng.classpath" value="testng.fasttest.classpath" />
-
-        <run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/>
-    </target>
-
-    <!-- A target that runs a test without doing ANY compilation or any extra work at all -->
-    <!-- Intended to enable parallel tests that share the same working directory and build -->
-    <target name="runtestonly">
-        <condition property="not.clean">
-            <and>
-                <available file="${build.dir}" />
-                <available file="${lib.dir}" />
-                <available file="${dist.dir}" />
-                <available file="${java.test.classes}" />
-            </and>
-        </condition>
-        <fail message="runtestonly target requires a NON-CLEAN working directory (INCLUDING test classes). Do a full test build using ant test.compile first." unless="not.clean" />
-
-        <condition property="no.single.test.specified">
-            <equals arg1="${single}" arg2="$${single}" />
-        </condition>
-        <fail message="Must specify a specific test. Usage: ant runtestonly -Dsingle=TestClass" if="no.single.test.specified" />
-
-        <property name="testng.classpath" value="testng.default.classpath" />
-        <property name="test.maxmemory" value="${test.default.maxmemory}"/>
-        <property name="include.scala" value="true" />
-
-        <run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/>
-    </target>
-
-</project>
diff --git a/ivy.xml b/ivy.xml
deleted file mode 100644
index 2e45247ab..000000000
--- a/ivy.xml
+++ /dev/null
@@ -1,117 +0,0 @@
-<!--
-  ~ Copyright (c) 2012, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="Sting"/>
-    <configurations>
-        <conf name="default" description="the core dependencies for the GATK"/>
-    </configurations>
-    <dependencies defaultconf="default">
-        <dependency org="net.sf" name="sam" rev="latest.integration"/>
-        <dependency org="net.sf" name="picard" rev="latest.integration"/>
-        <dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration"/>
-
-        <!-- Tribble -->
-        <dependency org="org.broad" name="tribble" rev="latest.integration"/>
-
-        <!-- Variant -->
-        <dependency org="org.broadinstitute" name="variant" rev="latest.integration"/>
-
-        <dependency org="log4j" name="log4j" rev="1.2.15"/>
-        <dependency org="javax.mail" name="mail" rev="1.4.4"/>
-        <dependency org="colt" name="colt" rev="1.2.0"/>
-        <dependency org="it.unimi.dsi" name="fastutil" rev="6.5.3" />
-
-        <!-- <dependency org="jboss" name="javassist" rev="3.7.ga"/> -->
-        <dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>
-        <dependency org="org.apache.bcel" name="bcel" rev="5.2"/>
-
-        <!-- Dependencies for reflections mvn repository -->
-        <dependency org="org.reflections" name="reflections" rev="0.9.8"/>
-        <dependency org="org.slf4j" name="slf4j-log4j12" rev="1.6.1"/>
-
-        <!-- Matrix package from math.nist.gov -->
-        <dependency org="gov.nist" name="Jama" rev="1.0.2"/>
-
-        <!-- Dependencies for the graph aligner -->
-        <dependency org="net.sf.jgrapht" name="jgrapht" rev="0.8.3"/>
-
-        <!-- Dependencies for the html walker documention -->
-        <dependency org="org.freemarker" name="freemarker" rev="2.3.18"/>
-
-        <!-- Commons Dependencies -->
-        <dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
-        <dependency org="org.apache.commons" name="commons-jexl" rev="2.1.1"/>
-        <dependency org="commons-lang" name="commons-lang" rev="2.5"/>
-        <dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
-        <dependency org="commons-io" name="commons-io" rev="2.1"/>
-        <dependency org="commons-collections" name="commons-collections" rev="3.2.1"/>
-        <dependency org="org.apache.commons" name="commons-math" rev="2.2"/>
-
-        <!-- Lucene core utilities -->
-        <!-- <dependency org="org.apache.lucene" name="lucene-core" rev="3.0.3"/> -->
-
-        <!-- Dependencies for LSF, DRMAA, and other C libraries -->
-        <dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>
-
-        <!-- Dependencies for amazon.com S3 support -->
-        <dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.1"/>
-
-        <!-- Dependencies for GridEngine -->
-        <dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
-
-        <!-- Scala dependancies -->
-        <dependency org="org.scala-lang" name="scala-compiler" rev="2.10.2"/>
-        <dependency org="org.scala-lang" name="scala-library" rev="2.10.2"/>
-
-        <!-- testing and evaluation dependencies -->
-        <dependency org="org.testng" name="testng" rev="6.8"/>
-        <dependency org="org.uncommons" name="reportng" rev="1.1.2"/>
-        <dependency org="com.google.caliper" name="caliper" rev="0.5-rc1"/>
-		<dependency org="com.google.inject" name="guice" rev="3.0"/>
-
-        <!-- Contracts for Java and dependencies -->
-        <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/>
-        <dependency org="asm" name="asm-all" rev="3.3.1"/>
-
-        <!-- POI, for reading pipeline files -->
-        <dependency org="org.apache.poi" name="poi" rev="3.8-beta3"/>
-        <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3"/>
-
-        <!-- snpEff annotator for pipelines -->
-        <dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5"/>
-
-        <!-- MongoDB for the GXDB project -->
-        <dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/>
-
-        <!-- GSON and HTTP for talking to the REST API on Vanilla Forums -->
-        <dependency org="com.google.code.gson" name="gson" rev="2.2.2"/>
-        <dependency org="org.apache.httpcomponents" name="httpclient" rev="4.1.1"/>
-
-        <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
-        <exclude org="javax.servlet"/>
-        <exclude org="javax.jms"/>
-        <exclude org="com.sun.*"/>
-    </dependencies>
-</ivy-module>
diff --git a/public/packages/Aligner.xml b/public/packages/Aligner.xml
deleted file mode 100644
index 031dfacfd..000000000
--- a/public/packages/Aligner.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="Aligner">
-  <executable name="Aligner">
-    <dependencies>
-      <!-- BWA/C aligner implementation -->
-      <class name="org.broadinstitute.sting.alignment.bwa.c.BWACAligner" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/CreatePackager.xsl b/public/packages/CreatePackager.xsl
deleted file mode 100644
index a89b6bb35..000000000
--- a/public/packages/CreatePackager.xsl
+++ /dev/null
@@ -1,220 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
-
-  <xsl:variable name="ant.basedir" select="'${basedir}'" />
-  <xsl:variable name="sting.dir" select="'${sting.dir}/'" />
-  <xsl:variable name="classpath" select="'${sting.dir}/staging:${additional.jars}'" />
-  <xsl:variable name="dist.dir" select="'${sting.dir}/dist'" />
-  <xsl:variable name="staging.dir" select="'${sting.dir}/staging'" />
-  <xsl:variable name="package.basename" select="'${package.basename}'" />
-  <xsl:variable name="package.dir" select="'${package.dir}'" />
-  <xsl:variable name="package.filename" select="'${package.filename}'" />
-  <xsl:variable name="resources.dir" select="'${package.dir}/resources'" />
-  
-<xsl:template match="package">
-  <xsl:output method="xml" indent="yes"/>
-
-  <project name="{@name}" default="package">
-
-    <property name="sting.dir" value="{$ant.basedir}" />
-    <!-- Read version information out of the xml file -->
-    <xsl:choose>
-      <xsl:when test="version/@property">
-	<xsl:variable name="version.property" select="concat('${',version/@property,'}')" />
-	<property file="{$staging.dir}/{version/@file}" />
-	<property name="package.basename" value="{concat(@name,'-',$version.property)}" />
-      </xsl:when>
-      <xsl:otherwise>
-	<property name="package.basename" value="{@name}" />
-      </xsl:otherwise>
-    </xsl:choose>
-    <property name="package.dir" value="{concat($dist.dir,'/packages/',$package.basename)}" />
-    <property name="package.filename" value="{concat($package.basename,'.tar.bz2')}" />
-
-    <target name="package">
-      <!-- Verify that all classes specified are present -->
-      <xsl:for-each select="//class">
-	<available property="is.{@name}.present" classpath="{$classpath}" classname="{@name}"/>
-	<fail message="Class {@name} not found" unless="is.{@name}.present" />
-      </xsl:for-each>
-      <xsl:for-each select="//resource-bundle">
-	<available property="is.{@file}.present" file="{$staging.dir}/{@file}"/>
-	<fail message="Resource bundle {@file} not found" unless="is.{@file}.present" />
-      </xsl:for-each>
-
-      <!-- Verify that all files specified are present -->
-      <xsl:for-each select="//dependencies/file">
-        <xsl:choose>
-          <xsl:when test="@name">
-            <available property="is.{@name}.present" file="{$staging.dir}/{@name}" type="file"/>
-            <fail message="File dependency {@name} not found" unless="is.{@name}.present" />
-          </xsl:when>
-          <xsl:when test="@path">
-            <available property="is.{@path}.present" file="{$staging.dir}/{@path}" type="file"/>
-            <fail message="File dependency {@path} not found" unless="is.{@path}.present" />
-          </xsl:when>
-          <xsl:otherwise>
-            <fail message="File dependency must specify a name or a path"/>
-          </xsl:otherwise>
-        </xsl:choose>
-      </xsl:for-each>
-      <xsl:for-each select="//dependencies/dir">
-        <available property="is.{@name}.present" file="{$staging.dir}/{@name}" type="dir"/>
-        <fail message="Directory {@name} not found" unless="is.{@name}.present" />
-      </xsl:for-each>
-
-      <!-- Create an output directory for the package -->
-      <mkdir dir="{$package.dir}"/>
-
-      <!-- Create the executable sections -->
-      <xsl:apply-templates select="executable" />
-
-      <!-- Add in other modules -->
-      <xsl:for-each select="modules/module">
-	<xsl:apply-templates select="document(@file)/package/executable" />
-      </xsl:for-each>
-
-      <!-- Include various resource files explicitly specified in this file and in all other modules -->
-      <xsl:apply-templates select="resources" />
-      <xsl:for-each select="//modules/module">
-	<xsl:apply-templates select="document(@file)/package/resources" />
-      </xsl:for-each>
-
-      <!-- Bundle the package into a single zip file -->
-      <tar destfile="{$dist.dir}/packages/{$package.filename}" compression="bzip2">
-        <fileset dir="{$dist.dir}/packages" includes="{$package.basename}/**"/>
-      </tar>
-    </target>
-
-    <target name="release">
-      <xsl:for-each select="release/executable">
-	<copy todir="{@directory}/{$package.basename}"><fileset dir="{$package.dir}" /></copy>
-	<xsl:if test="@symlink">
-	  <symlink link="{@directory}/{@symlink}" resource="{$package.basename}" overwrite="true" />	
-	</xsl:if>
-      </xsl:for-each>
-      <xsl:for-each select="release/archive">
-	<copy file="{$dist.dir}/packages/{$package.filename}" todir="{@directory}" />
-	<xsl:if test="@symlink">
-	  <symlink link="{@directory}/{@symlink}" resource="{$package.filename}" overwrite="true" />	
-	</xsl:if>
-      </xsl:for-each>
-    </target>
-  </project>
-</xsl:template>
-
-<!-- Create a symlink for the given file in the given target directory -->
-<xsl:template name="symlink">
-  <xsl:param name="file.name" />
-  <xsl:param name="target.dir" />
-  <xsl:variable name="short.name">
-    <xsl:call-template name="get-short-name">
-      <xsl:with-param name="string" select="$file.name" />
-    </xsl:call-template>
-  </xsl:variable>
-  <xsl:variable name="full.path">
-    <xsl:call-template name="get-full-path">
-      <xsl:with-param name="working-dir" select="$sting.dir"/>
-      <xsl:with-param name="file" select="$file.name" />
-    </xsl:call-template>
-  </xsl:variable>
-  <available property="is.{$short.name}.present" file="{$file.name}"/>
-  <fail message="File {$file.name} not found" unless="is.{$short.name}.present" />
-  <delete file="{$target.dir}/{$short.name}" />
-  <symlink link="{$target.dir}/{$short.name}" resource="{$full.path}" overwrite="true" />
-</xsl:template>
-
-<!-- Transform an executable tag into an ant 'jar' task with nested fileset -->
-<xsl:template match="executable">
-  <!-- Create a jar file containing the specified classes / packages and all their dependencies -->
-  <jar jarfile="{$package.dir}/{@name}.jar">
-    <classfileset dir="{$staging.dir}">
-      <root classname="{main-class/@name}"/>
-    </classfileset>
-    <xsl:for-each select="resource-bundle">
-      <fileset file="{$staging.dir}/{@file}" />
-    </xsl:for-each>
-    <xsl:for-each select="modules/module">
-      <xsl:apply-templates select="document(@file)/package/executable/dependencies" />
-    </xsl:for-each>
-    <xsl:apply-templates select="dependencies" />
-    <manifest>
-      <attribute name="Main-Class" value="{main-class/@name}"/>
-    </manifest>
-  </jar>
-</xsl:template>
-
-<!-- Transform a resource file into a symlink operation -->
-<xsl:template match="resources">
-  <xsl:for-each select="file">
-    <mkdir dir="{$resources.dir}"/>
-    <xsl:call-template name="symlink">
-      <xsl:with-param name="file.name" select="@name" />
-      <xsl:with-param name="target.dir" select="$resources.dir" />
-    </xsl:call-template>
-  </xsl:for-each>
-</xsl:template>
-
-<!-- Transform a dependency list into a fileset for embedding in a jar -->
-<xsl:template match="dependencies">
-  <classfileset dir="{$staging.dir}">
-    <xsl:for-each select="package">
-      <rootfileset dir="{$staging.dir}" includes="{concat(translate(@name,'.','/'),'/','*.class')}" />
-    </xsl:for-each>
-    <xsl:for-each select="class">
-      <root classname="{@name}" />
-    </xsl:for-each>
-  </classfileset>
-  <xsl:for-each select="file">
-    <xsl:choose>
-      <xsl:when test="@name">
-        <fileset file="{$staging.dir}/{@name}" />
-      </xsl:when>
-      <xsl:when test="@path">
-        <fileset dir="{$staging.dir}">
-          <xsl:attribute name="includes">
-            <xsl:value-of select="@path"/>
-          </xsl:attribute>
-        </fileset>
-      </xsl:when>
-    </xsl:choose>
-  </xsl:for-each>
-  <xsl:for-each select="dir">
-    <xsl:variable name="includes">
-      <xsl:choose>
-        <xsl:when test="@includes = ''">
-          <xsl:value-of select="concat(@name,'/**')"/>
-        </xsl:when>
-        <xsl:otherwise>
-          <xsl:value-of select="concat(@name,'/',@includes)"/>
-        </xsl:otherwise>
-      </xsl:choose>
-    </xsl:variable>
-    <fileset dir="{$staging.dir}" includes="{$includes}"/>
-  </xsl:for-each>
-</xsl:template>
-
-<!-- Determine the short name (filename w/o directory structure of the given filename -->
-<xsl:template name="get-short-name">
-  <xsl:param name="string"/>
-  <xsl:choose>
-    <xsl:when test="contains($string,'/')">
-      <xsl:call-template name="get-short-name">
-        <xsl:with-param name="string" select="substring-after($string,'/')" />
-      </xsl:call-template>
-    </xsl:when>
-    <xsl:otherwise><xsl:value-of select="$string"/></xsl:otherwise>
-  </xsl:choose>    
-</xsl:template>
-
-<!-- Determine the full path of the given filename.  Take into account absolute / relative paths -->
-<xsl:template name="get-full-path">
-  <xsl:param name="working-dir"/>
-  <xsl:param name="file"/>
-  <xsl:choose>
-    <xsl:when test="starts-with($file,'/')"><xsl:value-of select="$file"/></xsl:when>
-    <xsl:otherwise><xsl:value-of select="concat($working-dir,$file)"/></xsl:otherwise>
-  </xsl:choose>
-</xsl:template>
-
-</xsl:stylesheet>
diff --git a/public/packages/GATKEngine.xml b/public/packages/GATKEngine.xml
deleted file mode 100644
index 08d2e1c2c..000000000
--- a/public/packages/GATKEngine.xml
+++ /dev/null
@@ -1,62 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ Copyright (c) 2011, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<package name="GATKEngine">
-  <executable name="GATKEngine">
-    <dependencies>
-      <!-- Package everything in org.broadinstitute.sting -->
-      <package name="org.broadinstitute.sting.**" />
-      <!-- Tribble codecs -->
-      <package name="org.broad.tribble.**" />
-      <!-- The variant package (VCF, BCF, and VariantContext) -->
-      <package name="org.broadinstitute.variant.**" />
-      <!-- Workaround - depend on the logger impl required by JEXL -->
-      <package name="org.apache.commons.logging.impl" />
-      <!-- R packages -->
-      <dir name="org/broadinstitute/sting/utils/R" includes="**/*.tar.gz" />
-      <!-- All R scripts in org.broadinstitute.sting -->
-      <dir name="org/broadinstitute/sting" includes="**/*.R" />
-      <!-- Resources in org.broadinstitute.sting -->
-      <dir name="org/broadinstitute/sting" includes="**/resources/*" />
-      <dir name="org/broadinstitute/sting" includes="**/templates/*" />
-      <!-- The GATK public key -->
-      <file path="GATK_public.key" />
-    </dependencies>
-  </executable>
-  <resources>
-    <!-- Sample reads and reference files -->
-    <file name="public/testdata/exampleBAM.bam" />
-    <file name="public/testdata/exampleBAM.bam.bai" />
-    <file name="public/testdata/exampleFASTA.fasta" />
-    <file name="public/testdata/exampleFASTA.fasta.fai" />
-    <file name="public/testdata/exampleFASTA.dict" />
-    <!-- GATK sample code and build scripts -->
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java" />
-  </resources>
-</package>
diff --git a/public/packages/GenomeAnalysisTK.xml b/public/packages/GenomeAnalysisTK.xml
deleted file mode 100644
index e95c992b6..000000000
--- a/public/packages/GenomeAnalysisTK.xml
+++ /dev/null
@@ -1,40 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ Copyright (c) 2012, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<!-- The full release of the GATK contains both public and protected tools (but nothing from private) -->
-<package name="GenomeAnalysisTK">
-  <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
-  <executable name="GenomeAnalysisTK">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <modules>
-      <module file="GATKEngine.xml"/>
-    </modules>
-  </executable>
-  <release>
-    <executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />
-    <archive directory="/humgen/gsa-hpprojects/GATK/bin" symlink="GenomeAnalysisTK-latest.tar.bz2" />
-  </release>
-</package>
diff --git a/public/packages/PicardPrivate.xml b/public/packages/PicardPrivate.xml
deleted file mode 100644
index d898a5d07..000000000
--- a/public/packages/PicardPrivate.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="picard-private-parts">
-  <executable name="picard-private-parts">
-    <dependencies>
-      <class name="edu.mit.broad.picard.util.PicardAggregationFsUtil" />
-      <class name="edu.mit.broad.picard.genotype.fingerprint.v2.FingerprintingSummaryMetrics" />
-      <class name="edu.mit.broad.picard.genotype.concordance.DbSnpMatchMetrics" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/Queue.xml b/public/packages/Queue.xml
deleted file mode 100644
index 621a549d5..000000000
--- a/public/packages/Queue.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ Copyright (c) 2011, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<!-- The full release of Queue contains both public and protected tools (but nothing from private) -->
-<package name="Queue">
-    <version file="StingText.properties" property="org.broadinstitute.sting.queue.version" />
-    <executable name="Queue">
-        <main-class name="org.broadinstitute.sting.queue.QCommandLine" />
-        <resource-bundle file="StingText.properties" />
-        <modules>
-            <module file="QueueEngine.xml"/>
-            <module file="GATKEngine.xml"/>
-        </modules>
-    </executable>
-    <release>
-        <executable directory="/humgen/gsa-hpprojects/Queue/bin" symlink="current" />
-        <archive directory="/humgen/gsa-hpprojects/Queue/bin" symlink="Queue-latest.tar.bz2" />
-    </release>
-</package>
diff --git a/public/packages/QueueEngine.xml b/public/packages/QueueEngine.xml
deleted file mode 100644
index af3e20219..000000000
--- a/public/packages/QueueEngine.xml
+++ /dev/null
@@ -1,78 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ Copyright (c) 2012, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<package name="QueueEngine">
-    <executable name="QueueEngine">
-        <dependencies>
-            <!-- Queue -->
-            <package name="org.broadinstitute.sting.queue.**" />
-
-            <!-- Pipeline + Utils -->
-            <package name="org.broadinstitute.sting.pipeline.**" />
-            <package name="org.broadinstitute.sting.utils.**" />
-
-            <!-- Scala -->
-            <package name="scala.**" />
-
-            <!-- Picard -->
-            <package name="net.sf.picard.**" />
-            <package name="edu.mit.broad.picard.**" />
-
-            <!-- JavaMail -->
-            <package name="javax.activation.**" />
-            <package name="javax.mail.**" />
-            <package name="com.sun.activation.**" />
-            <package name="com.sun.mail.**" />
-            <file path="META-INF/javamail.charset.map" />
-            <file path="META-INF/javamail.default.address.map" />
-            <file path="META-INF/javamail.default.providers" />
-            <file path="META-INF/mailcap" />
-            <file path="META-INF/mailcap.default" />
-            <file path="META-INF/mimetypes.default" />
-
-            <!-- JNA, including embedded native libraries -->
-            <dir name="com/sun/jna" />
-
-            <!-- Contracts for Java -->
-            <package name="com.google.java.contract.**" />
-
-            <!-- snpEff -->
-            <package name="ca.mcgill.mcb.pcingola.**" />
-            <file path="snpEff_genes.ftl" />
-            <file path="snpEff_summary.ftl" />
-            
-            <!-- R scripts -->
-            <dir name="org/broadinstitute/sting/queue" includes="**/*.R" />
-        </dependencies>
-    </executable>
-    <resources>
-        <!-- Sample QScripts -->
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala" />
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala" />
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala" />
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala" />
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala" />
-    </resources>
-</package>
diff --git a/settings/ivysettings.properties b/settings/ivysettings.properties
deleted file mode 100644
index 8a67434f9..000000000
--- a/settings/ivysettings.properties
+++ /dev/null
@@ -1 +0,0 @@
-repository.dir=${ivy.settings.dir}/repository
diff --git a/settings/ivysettings.xml b/settings/ivysettings.xml
deleted file mode 100644
index ce7667140..000000000
--- a/settings/ivysettings.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<ivysettings>
-  <properties file="${ivy.settings.dir}/ivysettings.properties"/>
-  <settings defaultResolver="chain"/>
-  <resolvers>
-    <chain name="chain">
-      <filesystem name="projects">
-	<artifact pattern="${repository.dir}/[organisation]/[artifact]-[revision].[ext]" />
-	<ivy pattern="${repository.dir}/[organisation]/[module]-[revision].xml" />
-      </filesystem>
-      <ibiblio name="maven" root="http://repo1.maven.org/maven2" m2compatible="true" />
-    </chain>
-  </resolvers>
-</ivysettings>