diff --git a/ivy.xml b/ivy.xml
index 3c0b7aebe..46f2d46fa 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -18,7 +18,7 @@
     <dependency org="org.broad" name="tribble" rev="latest.integration" conf="default"/>
     
     <!-- Dependencies for reflections mvn repository -->
-    <dependency org="org.reflections" name="reflections" rev="0.9.5-svnversion79" conf="default"/>
+    <dependency org="org.reflections" name="reflections" rev="0.9.5-svnversion79M" 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"/>
diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
index d5e676356..45a344c98 100755
--- a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
@@ -26,11 +26,14 @@
 package org.broadinstitute.sting.utils.classloader;
 
 import org.reflections.Reflections;
+import org.reflections.scanners.ResourcesScanner;
 import org.reflections.scanners.SubTypesScanner;
 import org.reflections.util.ClasspathHelper;
 import org.reflections.util.ConfigurationBuilder;
+import org.reflections.util.ManifestAwareClasspathHelper;
 import org.slf4j.LoggerFactory;
 
+import java.net.URL;
 import java.util.Set;
 import java.util.ArrayList;
 import java.util.List;
@@ -46,11 +49,11 @@ public class PackageUtils {
     private static Reflections reflections = null;
 
     static {
-
+        List<URL> urls = ManifestAwareClasspathHelper.getUrlsForManifestCurrentClasspath();
         // Initialize general-purpose source tree reflector.
         reflections = new Reflections( new ConfigurationBuilder()
-                .setUrls(ClasspathHelper.getUrlsForCurrentClasspath())
-                .setScanners(new SubTypesScanner()));
+                .setUrls(urls)
+                .setScanners(new SubTypesScanner(),new ResourcesScanner()));
     }
 
     /**
diff --git a/settings/repository/org.reflections/reflections-0.9.5-svnversion79.jar b/settings/repository/org.reflections/reflections-0.9.5-svnversion79M.jar
similarity index 84%
rename from settings/repository/org.reflections/reflections-0.9.5-svnversion79.jar
rename to settings/repository/org.reflections/reflections-0.9.5-svnversion79M.jar
index 2b391eddf..32b740a57 100644
Binary files a/settings/repository/org.reflections/reflections-0.9.5-svnversion79.jar and b/settings/repository/org.reflections/reflections-0.9.5-svnversion79M.jar differ
diff --git a/settings/repository/org.reflections/reflections-0.9.5-svnversion79.xml b/settings/repository/org.reflections/reflections-0.9.5-svnversion79M.xml
similarity index 68%
rename from settings/repository/org.reflections/reflections-0.9.5-svnversion79.xml
rename to settings/repository/org.reflections/reflections-0.9.5-svnversion79M.xml
index 690c10f29..376e8e71d 100644
--- a/settings/repository/org.reflections/reflections-0.9.5-svnversion79.xml
+++ b/settings/repository/org.reflections/reflections-0.9.5-svnversion79M.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.reflections" module="reflections" revision="0.9.5-svnversion79" status="release" />
+    <info organisation="org.reflections" module="reflections" revision="0.9.5-svnversion79M" status="release" />
 </ivy-module>