diff --git a/build.xml b/build.xml
index 4db71a9ab..cc45467d8 100644
--- a/build.xml
+++ b/build.xml
@@ -185,10 +185,7 @@
         <include name="**/*.class"/>
     </fileset>
 
-    <patternset id="dependency.mask" includes="*.jar">
-        <exclude name="testng*.jar" />
-        <exclude name="bcel*.jar" />
-    </patternset>
+    <patternset id="dependency.mask" includes="*.jar" />
 
     <path id="external.dependencies">
         <fileset dir="${lib.dir}" erroronmissingdir="false">
@@ -205,6 +202,16 @@
         <pathelement location="${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>
@@ -240,13 +247,6 @@
         </fileset>
     </path>
 
-    <path id="build.results">
-        <fileset dir="${dist.dir}">
-            <patternset refid="dependency.mask" />
-         </fileset>
-    </path>
-
-
     <!-- ******************************************************************************** -->
     <!-- Ivy Retrieve                                                                     -->
     <!-- ******************************************************************************** -->
@@ -1110,15 +1110,10 @@
     </path>
 
     <path id="testng.default.classpath">
-        <pathelement location="${java.classes}" />
-        <pathelement location="${scala.classes}" />
+        <path refid="build.results" />
         <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>
 
     <!-- Test targets -->
@@ -1126,9 +1121,6 @@
     <target name="test.init.compile">
         <mkdir dir="${java.test.classes}"/>
         <mkdir dir="${scala.test.classes}"/>
-        <antcall target="resolve">
-          <param name="ivy.conf" value="test"/>
-        </antcall>
     </target>
 
    <target name="test.java.internal.compile" depends="dist,test.init.compile">
@@ -1136,10 +1128,8 @@
         <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="external.dependencies" />
-                <pathelement location="${java.classes}"/>
+                <path refid="build.results" />
                 <pathelement location="${java.contracts.dir}"/>
-                <pathelement location="${testng.jar}"/>
             </classpath>
             <compilerarg value="-proc:none"/>
         </javac>
@@ -1150,11 +1140,9 @@
         <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}" srcdir="${external.dir}">
             <include name="*/test/**/*.java"/>
             <classpath>
-                <path refid="external.dependencies" />
+                <path refid="build.results" />
                 <pathelement location="${java.test.classes}"/>
-                <pathelement location="${java.classes}"/>
                 <pathelement location="${java.contracts.dir}"/>
-                <pathelement location="${testng.jar}"/>
             </classpath>
             <compilerarg value="-proc:none"/>
         </javac>
@@ -1167,9 +1155,8 @@
         <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes">
 	        <src refid="scala.test.source.path" />
             <classpath>
-                <path refid="scala.dependencies"/>
+                <path refid="build.results"/>
                 <pathelement location="${java.test.classes}"/>
-                <pathelement location="${testng.jar}"/>
             </classpath>
         </scalac>
     </target>
@@ -1376,14 +1363,13 @@
 
     <!-- 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,test.init">
+    <target name="fasttest" depends="init.javaonly,init">
         <condition property="not.clean">
             <and>
                 <available file="${build.dir}" />
                 <available file="${lib.dir}" />
                 <available file="${dist.dir}" />
                 <available file="${java.test.classes}" />
-                <available file="${testng.jar}" />
             </and>
         </condition>
         <fail message="fasttest requires a NON-CLEAN working directory (INCLUDING test classes). Do a full test build using ant test.compile first." unless="not.clean" />
@@ -1401,13 +1387,27 @@
         <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
             <src refid="java.test.source.path" />
             <classpath>
-                <path refid="external.dependencies" />
                 <pathelement location="${java.classes}"/>
-                <pathelement location="${testng.jar}"/>
+                <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>
 </project>
diff --git a/ivy.xml b/ivy.xml
index 1d2f95dc1..b7ca65406 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -24,11 +24,8 @@
 
 <ivy-module version="1.0">
     <info organisation="org.broadinstitute" module="Sting"/>
-    <configurations defaultconfmapping="test->default">
+    <configurations>
         <conf name="default" description="the core dependencies for the GATK"/>
-        <conf name="test" extends="default" description="external dependencies used for testing and metrics"/>
-        <conf name="scala" extends="default" description="the dependencies for scala"/>
-        <conf name="queue" extends="scala" description="the dependencies for Queue"/>
     </configurations>
     <dependencies defaultconf="default">
         <dependency org="net.sf" name="sam" rev="latest.integration"/>
@@ -83,9 +80,9 @@
         <dependency org="org.scala-lang" name="scala-library" rev="2.9.2"/>
 
         <!-- testing and evaluation dependencies -->
-        <dependency org="org.testng" name="testng" rev="5.14.1" conf="test"/>
-        <dependency org="org.uncommons" name="reportng" rev="1.1.2" conf="test"/>
-        <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test"/>
+        <dependency org="org.testng" name="testng" rev="5.14.1"/>
+        <dependency org="org.uncommons" name="reportng" rev="1.1.2"/>
+        <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT"/>
 
         <!-- Contracts for Java and dependencies -->
         <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/>