diff --git a/ivy.xml b/ivy.xml
index 4f5e0cb3b..910effbbe 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -18,15 +18,22 @@
     <dependency org="org.broad" name="tribble" rev="latest.integration" conf="default"/>
     
     <!-- Dependencies for reflections mvn repository -->
-    <dependency org="org.reflections" name="reflections" rev="0.9.2" conf="default"/>
+    <dependency org="org.reflections" name="reflections" rev="0.9.5-svnversion79" conf="default"/>
     <dependency org="com.google.collections" name="google-collections" rev="0.9" conf="default"/>
+    <dependency org="javassist" name="javassist" rev="3.8.0.GA"/>
+    <dependency org="ch.qos.logback" name="logback-core" rev="0.9.9"/>
+    <dependency org="ch.qos.logback" name="logback-classic" rev="0.9.9"/>
+    <dependency org="org.slf4j" name="slf4j-api" rev="1.5.6"/>
+    <dependency org="xml-apis" name="xml-apis" rev="1.0.b2"/>
+    <dependency org="com.google.collections" name="google-collections" rev="1.0"/>
+    <dependency org="dom4j" name="dom4j" rev="1.6"/>
 
     <!-- Dependencies for the graph aligner -->  
-      <dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3" conf="default"/>
+    <dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3" conf="default"/>
      
     <!-- Dependencies for VariantFiltration -->  
-      <dependency org="commons-jexl" name="commons-jexl" rev="1.1" conf="default"/>
-      <dependency org="commons-logging" name="commons-logging" rev="1.1.1" conf="default"/>
+    <dependency org="commons-jexl" name="commons-jexl" rev="1.1" conf="default"/>
+    <dependency org="commons-logging" name="commons-logging" rev="1.1.1" conf="default"/>
      
     <!-- Scala dependancies -->
     <dependency org="org.scala-lang" name="scala-compiler" rev="2.7.7" conf="scala->default"/>
diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
index 3e760ba63..c45cdde24 100755
--- a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
@@ -27,9 +27,9 @@ package org.broadinstitute.sting.utils.classloader;
 
 import org.reflections.Reflections;
 import org.reflections.scanners.SubTypesScanner;
-import org.reflections.util.AbstractConfiguration;
 import org.reflections.util.ClasspathHelper;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.reflections.util.ConfigurationBuilder;
+import org.slf4j.LoggerFactory;
 
 import java.util.Set;
 import java.util.ArrayList;
@@ -45,13 +45,11 @@ public class PackageUtils {
     private static Reflections reflections = null;
 
     static {
+
         // Initialize general-purpose source tree reflector.
-        reflections = new Reflections( new AbstractConfiguration() {
-            {
-                setUrls(ClasspathHelper.getUrlsForCurrentClasspath());
-                setScanners(new SubTypesScanner());
-            }
-        });
+        reflections = new Reflections( new ConfigurationBuilder()
+                .setUrls(ClasspathHelper.getUrlsForCurrentClasspath())
+                .setScanners(new SubTypesScanner()));
     }
 
     /**
diff --git a/settings/repository/org.reflections/reflections-0.9.2.jar b/settings/repository/org.reflections/reflections-0.9.2.jar
deleted file mode 100644
index c91cffea5..000000000
Binary files a/settings/repository/org.reflections/reflections-0.9.2.jar and /dev/null differ
diff --git a/settings/repository/org.reflections/reflections-0.9.5-svnversion79.jar b/settings/repository/org.reflections/reflections-0.9.5-svnversion79.jar
new file mode 100644
index 000000000..2b391eddf
Binary files /dev/null and b/settings/repository/org.reflections/reflections-0.9.5-svnversion79.jar differ
diff --git a/settings/repository/org.reflections/reflections-0.9.2.xml b/settings/repository/org.reflections/reflections-0.9.5-svnversion79.xml
similarity index 68%
rename from settings/repository/org.reflections/reflections-0.9.2.xml
rename to settings/repository/org.reflections/reflections-0.9.5-svnversion79.xml
index 7676d4df8..690c10f29 100644
--- a/settings/repository/org.reflections/reflections-0.9.2.xml
+++ b/settings/repository/org.reflections/reflections-0.9.5-svnversion79.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.reflections" module="reflections" revision="0.9.2" status="release" />
+    <info organisation="org.reflections" module="reflections" revision="0.9.5-svnversion79" status="release" />
 </ivy-module>