diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java
index e81ab21e9..f95c12690 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/DocumentedGATKFeatureHandler.java
@@ -72,7 +72,7 @@ public abstract class DocumentedGATKFeatureHandler {
      * @return
      */
     public String getDestinationFilename(ClassDoc doc, Class clazz) {
-        return GATKDocUtils.phpFilenameForClass(clazz);
+        return GATKDocUtils.phpFilenameForClass(clazz, GATKDoclet.outputFileExtension);
     }
 
     /**
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java
index 72aba4da7..8ff7e58f3 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDocUtils.java
@@ -50,7 +50,11 @@ public class GATKDocUtils {
      * @return
      */
     public static String phpFilenameForClass(Class c) {
-        return c.getName().replace(".", "_") + ".php";
+        return phpFilenameForClass(c, "php");
+    }
+
+    public static String phpFilenameForClass(Class c, String extension) {
+        return c.getName().replace(".", "_") + "." + extension;
     }
 
     /**
diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java
index af56eb9b2..afae1bb6e 100644
--- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java
+++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/help/GATKDoclet.java
@@ -25,12 +25,8 @@
 
 package org.broadinstitute.gatk.utils.help;
 
-import com.google.gson.ExclusionStrategy;
-import com.google.gson.FieldAttributes;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
-import com.google.gson.annotations.Expose;
-import com.google.gson.stream.JsonWriter;
 import com.sun.javadoc.ClassDoc;
 import com.sun.javadoc.RootDoc;
 import freemarker.template.Configuration;
@@ -82,6 +78,11 @@ public abstract class GATKDoclet {
     final protected static File DESTINATION_DIR = new File("gatkdocs");
 
     final private static String FORUM_KEY_PATH = "/local/gsa-engineering/gatkdocs_publisher/forum.key";
+
+    final private static String OUTPUT_FILE_EXTENSION = "php";
+
+    /** Controls the extension of the non-json output files, and also the HREFs to these files.  Default: php */
+    final private static String OUTPUT_FILE_EXTENSION_OPTION = "-output-file-extension";
     // ----------------------------------------------------------------------
     //
     // Global variables that are set on the command line by javadoc
@@ -92,6 +93,7 @@ public abstract class GATKDoclet {
     protected static String forumKeyPath = FORUM_KEY_PATH;
     protected static String buildTimestamp = null, absoluteVersion = null;
     protected static boolean showHiddenFeatures = false;
+    protected static String outputFileExtension = OUTPUT_FILE_EXTENSION;
 
     protected static boolean testOnly = false;
 
@@ -148,6 +150,9 @@ public abstract class GATKDoclet {
                 showHiddenFeatures = true;
             if (options[0].equals("-test"))
                 testOnly = true;
+            if (options[0].equals(OUTPUT_FILE_EXTENSION_OPTION)) {
+                outputFileExtension = options[1];
+            }
         }
 
         if (!settingsDir.exists())
@@ -173,7 +178,8 @@ public abstract class GATKDoclet {
                 option.equals("-forum-key-path") ||
                 option.equals("-build-timestamp") ||
                 option.equals("-absolute-version") ||
-                option.equals("-include-hidden")) {
+                option.equals("-include-hidden") ||
+                option.equals(OUTPUT_FILE_EXTENSION_OPTION)) {
             return 2;
         } else if (option.equals("-test"))
             return 1;
@@ -392,7 +398,7 @@ public abstract class GATKDoclet {
         Template temp = cfg.getTemplate("generic.index.template.html");
 
         /* Merge data-model with template */
-        Writer out = new OutputStreamWriter(new FileOutputStream(new File(destinationDir + "/index.php")));
+        Writer out = new OutputStreamWriter(new FileOutputStream(new File(destinationDir + "/index." + outputFileExtension)));
         try {
             temp.process(groupIndexData(indexData), out);
             out.flush();