diff --git a/build.xml b/build.xml
index d95553efc..a79c4dbe9 100644
--- a/build.xml
+++ b/build.xml
@@ -35,7 +35,15 @@
 	<exclude name="**/oneoffprojects/**" unless="include.oneoffs" />
       </patternset>
     </dirset>
-    
+
+    <!-- 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="${source.dir}">
+            <include name="**/**/templates/*" />
+        </fileset>
+    </path>
+
     <patternset id="dependency.mask" includes="*.jar">
       <exclude name="junit*.jar" />
       <exclude name="bcel*.jar" />
@@ -138,8 +146,9 @@
         </jar>
 
         <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
+            <path refid="gatk.resources"/>
             <fileset dir="build">
-	      <include name="${resource.file}" />
+	          <include name="${resource.file}" />
               <include name="**/gatk/**/*.class" />
               <include name="**/alignment/**/*.class"/>
               <include name="**/oneoffprojects/**/*.class" />
diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java b/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
index 23b59e911..770c23998 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java
@@ -22,7 +22,7 @@ import java.util.Map;
  */
 public class VE2ReportFactory {
     // where templates are stored
-    public static final String ve2templateDir = "templates/VE2";
+    public static final String ve2templateDir = "templates/";
 
     // our default output type
     public static final VE2TemplateType defaultReportFormat = VE2TemplateType.Table;
@@ -71,11 +71,8 @@ public class VE2ReportFactory {
      */
     private static Template createTemplate(VE2TemplateType template) {
            Configuration cfg = new Configuration();
-           try {
-               cfg.setDirectoryForTemplateLoading(new File(ve2templateDir));
-           } catch (IOException e) {
-               throw new StingException("Unable to find template directory " + ve2templateDir,e);
-           }
+           cfg.setClassForTemplateLoading(VE2ReportFactory.class,ve2templateDir);
+
            cfg.setObjectWrapper(new DefaultObjectWrapper());
            Template temp = null;
            try {
diff --git a/templates/VE2/csv_readable.ftl b/java/src/org/broadinstitute/sting/playground/utils/report/templates/csv_readable.ftl
similarity index 100%
rename from templates/VE2/csv_readable.ftl
rename to java/src/org/broadinstitute/sting/playground/utils/report/templates/csv_readable.ftl
diff --git a/templates/VE2/grep_readable.ftl b/java/src/org/broadinstitute/sting/playground/utils/report/templates/grep_readable.ftl
similarity index 100%
rename from templates/VE2/grep_readable.ftl
rename to java/src/org/broadinstitute/sting/playground/utils/report/templates/grep_readable.ftl
diff --git a/templates/VE2/human_readable.ftl b/java/src/org/broadinstitute/sting/playground/utils/report/templates/human_readable.ftl
similarity index 100%
rename from templates/VE2/human_readable.ftl
rename to java/src/org/broadinstitute/sting/playground/utils/report/templates/human_readable.ftl