diff --git a/build.xml b/build.xml
index fc495f7cc..81e24f58f 100644
--- a/build.xml
+++ b/build.xml
@@ -520,6 +520,8 @@
             <fileset dir="${java.classes}">
               <include name="**/utils/codecs/**/*.class"/>
               <include name="**/utils/variantcontext/**/*.class"/>
+              <include name="**/UserException*.class"/>
+	      <include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
             </fileset>
         </jar>
     </target>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
index 5f8f19892..4a4f6f6af 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java
@@ -342,12 +342,12 @@ public class DiffEngine {
             return reader.readFromFile(file, maxElementsToRead);
     }
 
-    public static boolean simpleDiffFiles(File masterFile, File testFile, DiffEngine.SummaryReportParams params) {
+    public static boolean simpleDiffFiles(File masterFile, File testFile, int maxElementsToRead, DiffEngine.SummaryReportParams params) {
         DiffEngine diffEngine = new DiffEngine();
 
         if ( diffEngine.canRead(masterFile) && diffEngine.canRead(testFile) ) {
-            DiffElement master = diffEngine.createDiffableFromFile(masterFile);
-            DiffElement test = diffEngine.createDiffableFromFile(testFile);
+            DiffElement master = diffEngine.createDiffableFromFile(masterFile, maxElementsToRead);
+            DiffElement test = diffEngine.createDiffableFromFile(testFile, maxElementsToRead);
             List<Difference> diffs = diffEngine.diff(master, test);
             diffEngine.reportSummarizedDifferences(diffs, params);
             return true;
diff --git a/public/java/test/org/broadinstitute/sting/MD5DB.java b/public/java/test/org/broadinstitute/sting/MD5DB.java
index bea9eaec5..6f56fce4b 100644
--- a/public/java/test/org/broadinstitute/sting/MD5DB.java
+++ b/public/java/test/org/broadinstitute/sting/MD5DB.java
@@ -47,6 +47,7 @@ public class MD5DB {
     /**
      * Subdirectory under the ant build directory where we store integration test md5 results
      */
+    private static final int MAX_RECORDS_TO_READ = 10000;
     public static final String LOCAL_MD5_DB_DIR = "integrationtests";
     public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests";
 
@@ -232,7 +233,7 @@ public class MD5DB {
 
                     // inline differences
                     DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(System.out, 20, 10, 0);
-                    boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), params);
+                    boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), MAX_RECORDS_TO_READ, params);
                     if ( success )
                         System.out.printf("Note that the above list is not comprehensive.  At most 20 lines of output, and 10 specific differences will be listed.  Please use -T DiffObjects -R public/testdata/exampleFASTA.fasta -m %s -t %s to explore the differences more freely%n",
                                 pathToExpectedMD5File, pathToFileMD5File);