diff --git a/build.xml b/build.xml
index 51f39f7a3..6c1090ea4 100644
--- a/build.xml
+++ b/build.xml
@@ -79,6 +79,17 @@
         <patternset refid="java.source.pattern" />
     </fileset>
 
+    <!-- terrible hack to get gatkdocs to see all files --> 
+    <patternset id="all.java.source.pattern">
+        <include name="${java.public.source.dir}/**/*.java" />
+        <include name="${java.private.source.dir}/**/*.java" />
+    </patternset>
+
+    <fileset id="all.java.source.files" dir="${basedir}">
+        <patternset refid="all.java.source.pattern" />
+    </fileset>
+
+
     <fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
         <include name="**/*.java" />
     </fileset>
@@ -457,9 +468,8 @@
         </javadoc>
     </target>
 
-    <target name="gatkdocs" unless="uptodate.extracthelp" depends="gatk.compile"
+    <target name="gatkdocs" unless="uptodate.extracthelp"
 	        description="Extract help key/value pair file from the JavaDoc tags.">
-        <property name="gatk.target" value="private"/>
         <path id="doclet.classpath">
             <path refid="external.dependencies" />
             <pathelement location="${java.classes}" />
@@ -472,7 +482,7 @@
                  additionalparam="-private -build-timestamp &quot;${build.timestamp}&quot; -absolute-version ${build.version} -out ${basedir}/${resource.path} -quiet -J-Xdebug -J-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005">
             <sourcefiles>
                 <union>
-                    <fileset refid="java.source.files"/>
+                    <fileset refid="all.java.source.files"/>
                 </union>
             </sourcefiles>
         </javadoc>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
index 3726e8e02..f8a2de316 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
@@ -50,6 +50,9 @@ import java.util.*;
  * gatk all the parsed out information.  Pretty much anything dealing with the underlying system should go here,
  * the gatk engine should  deal with any data related information.
  */
+@DocumentedGATKFeature(
+        groupName = "GATK Engine",
+        summary = "Features and arguments for the GATK engine itself, available to all walkers." )
 public class CommandLineGATK extends CommandLineExecutable {
     @Argument(fullName = "analysis_type", shortName = "T", doc = "Type of analysis to run")
     private String analysisName = null;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
index 003d9cd42..bf3ce352a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java
@@ -7,6 +7,9 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 /**
  * A SamRecordFilter that also depends on the header.
  */
+@DocumentedGATKFeature(
+        groupName = "Read filters",
+        summary = "GATK Engine arguments that filter or transfer incoming SAM/BAM data files" )
 public abstract class ReadFilter implements SamRecordFilter {
     /**
      * Sets the header for use by this filter.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java
index ff3b6d82f..5f11686a1 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java
@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import net.sf.picard.filter.SamRecordFilter;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.lang.annotation.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
index 9f26c9286..a5d2cd5b3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
@@ -46,7 +46,9 @@ import java.util.List;
 @ReadFilters(MalformedReadFilter.class)
 @PartitionBy(PartitionType.NONE)
 @BAQMode(QualityMode = BAQ.QualityMode.OVERWRITE_QUALS, ApplicationTime = BAQ.ApplicationTime.ON_INPUT)
-@DocumentedGATKFeature( groupName = "GATK walkers" )
+@DocumentedGATKFeature(
+        groupName = "GATK walkers",
+        summary = "General tools available for running on the command line as part of the GATK package" )
 public abstract class Walker<MapType, ReduceType> {
     final protected static Logger logger = Logger.getLogger(Walker.class);
     private GenomeAnalysisEngine toolkit;
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 7eab6f6c9..3c3299ff5 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -29,6 +29,7 @@ import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.File;
@@ -43,6 +44,9 @@ import java.util.Arrays;
  * Date: Sep 3, 2010
  * Time: 2:24:09 PM
  */
+@DocumentedGATKFeature(
+        groupName = "User exceptions",
+        summary = "Exceptions caused by incorrect user behavior, such as bad files, bad arguments, etc." )
 public class UserException extends ReviewedStingException {
     public UserException(String msg) { super(msg); }
     public UserException(String msg, Throwable e) { super(msg, e); }
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java
index a63869cad..689d1b7ad 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeature.java
@@ -36,6 +36,8 @@ import java.lang.annotation.*;
 @Retention(RetentionPolicy.RUNTIME)
 @Target(ElementType.TYPE)
 public @interface DocumentedGATKFeature {
+    boolean enable() default true;
     String groupName();
+    String summary() default "";
     Class<? extends DocumentedGATKFeatureHandler> handler() default GenericDocumentationHandler.class;
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
index fe3e56efe..ddcc12ab3 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java
@@ -25,24 +25,9 @@
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.javadoc.ClassDoc;
-import com.sun.javadoc.FieldDoc;
 import com.sun.javadoc.RootDoc;
-import com.sun.javadoc.Tag;
-import freemarker.template.Configuration;
-import freemarker.template.DefaultObjectWrapper;
-import freemarker.template.Template;
-import freemarker.template.TemplateException;
-import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
-import java.lang.reflect.Field;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
 
 /**
  *
@@ -50,6 +35,7 @@ import java.util.Map;
 public abstract class DocumentedGATKFeatureHandler {
     private GATKDoclet doclet;
     private String groupName;
+    private DocumentedGATKFeature annotation;
 
     protected RootDoc getRootDoc() {
         return this.doclet.rootDoc;
@@ -59,10 +45,18 @@ public abstract class DocumentedGATKFeatureHandler {
         this.doclet = doclet;
     }
 
+    public DocumentedGATKFeature getAnnotation() {
+        return annotation;
+    }
+
+    public void setAnnotation(DocumentedGATKFeature annotation) {
+        this.annotation = annotation;
+    }
+
     public boolean shouldBeProcessed(ClassDoc doc) { return true; }
 
     public String getDestinationFilename(ClassDoc doc) {
-        return ResourceBundleExtractorDoclet.getClassName(doc).replace(".", "_") + ".html";
+        return HelpUtils.getClassName(doc).replace(".", "_") + ".html";
     }
 
     final public String getGroupName() {
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
index 81eaf632c..ae8ab2c06 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
@@ -109,16 +109,18 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
             cfg.setObjectWrapper(new DefaultObjectWrapper());
 
             List<DocumentationData> indexData = new ArrayList<DocumentationData>();
+            Set<DocumentedGATKFeature> docFeatures = new HashSet<DocumentedGATKFeature>();
             for ( ClassDoc doc : rootDoc.classes() ) {
                 System.out.printf("Considering %s%n", doc);
                 DocumentedGATKFeatureHandler handler = getHandlerForClassDoc(doc);
                 if ( handler != null && handler.shouldBeProcessed(doc) ) {
                     DocumentationData docData = processDocumentationWithHandler(cfg, handler, doc);
+                    docFeatures.add(handler.getAnnotation());
                     indexData.add(docData);
                 }
             }
 
-            processIndex(cfg, indexData);
+            processIndex(cfg, indexData, new ArrayList<DocumentedGATKFeature>(docFeatures));
         } catch ( FileNotFoundException e ) {
             throw new RuntimeException(e);
         } catch ( IOException e ) {
@@ -129,13 +131,19 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
     private DocumentedGATKFeatureHandler getHandlerForClassDoc(ClassDoc doc) {
         try {
             // todo -- what do I need the ? extends Object to pass the compiler?
-            Class<? extends Object> docClass = ResourceBundleExtractorDoclet.getClassForDoc(doc);
+            Class<? extends Object> docClass = HelpUtils.getClassForDoc(doc);
             if ( docClass.isAnnotationPresent(DocumentedGATKFeature.class) ) {
                 DocumentedGATKFeature feature = docClass.getAnnotation(DocumentedGATKFeature.class);
-                DocumentedGATKFeatureHandler handler = feature.handler().newInstance();
-                handler.setGroupName(feature.groupName());
-                handler.setDoclet(this);
-                return handler;
+                if ( feature.enable() ) {
+                    DocumentedGATKFeatureHandler handler = feature.handler().newInstance();
+                    handler.setGroupName(feature.groupName());
+                    handler.setDoclet(this);
+                    handler.setAnnotation(feature);
+                    return handler;
+                } else {
+                    logger.info("Skipping disabled Documentation for " + doc);
+                    return null;
+                }
             } else {
                 return null; // not annotated so it shouldn't be documented
             }
@@ -152,21 +160,21 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
         }
     }
 
-    private void processIndex(Configuration cfg, List<DocumentationData> indexData) throws IOException {
+    private void processIndex(Configuration cfg, List<DocumentationData> indexData, List<DocumentedGATKFeature> docFeatures) throws IOException {
         /* Get or create a template */
         Template temp = cfg.getTemplate("generic.index.template.html");
 
         /* Merge data-model with template */
         Writer out = new OutputStreamWriter(new FileOutputStream(new File("testdoc/index.html")));
         try {
-            temp.process(groupIndexData(indexData), out);
+            temp.process(groupIndexData(indexData, docFeatures), out);
             out.flush();
         } catch ( TemplateException e ) {
             throw new ReviewedStingException("Failed to create GATK documentation", e);
         }
     }
 
-    private Map<String, Object> groupIndexData(List<DocumentationData> indexData) {
+    private Map<String, Object> groupIndexData(List<DocumentationData> indexData, List<DocumentedGATKFeature> docFeatures) {
         //
         // root -> data -> { summary -> y, filename -> z }, etc
         //      -> groups -> group1, group2, etc.
@@ -175,19 +183,28 @@ public class GATKDoclet extends ResourceBundleExtractorDoclet {
         Collections.sort(indexData);
 
         List<Map<String, String>> data = new ArrayList<Map<String, String>>();
-        Set<String> groups = new HashSet<String>();
-
         for ( DocumentationData indexDatum : indexData ) {
             data.add(indexDatum.toMap());
-            groups.add(indexDatum.group);
+        }
+
+        List<Map<String, String>> groups = new ArrayList<Map<String, String>>();
+        for ( DocumentedGATKFeature feature : docFeatures ) {
+            groups.add(toMap(feature));
         }
 
         root.put("data", data);
-        root.put("groups", new ArrayList<String>(groups));
+        root.put("groups", groups);
 
         return root;
     }
 
+    private static final Map<String, String> toMap(DocumentedGATKFeature annotation) {
+        Map<String, String> root = new HashMap<String, String>();
+        root.put("name", annotation.groupName());
+        root.put("summary", annotation.summary());
+        return root;
+    }
+
     private DocumentationData processDocumentationWithHandler(Configuration cfg,
                                                               DocumentedGATKFeatureHandler handler,
                                                               ClassDoc doc)
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
index cab6c327d..a4e3e5031 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
@@ -26,12 +26,7 @@ package org.broadinstitute.sting.utils.help;
 
 import com.sun.javadoc.ClassDoc;
 import com.sun.javadoc.FieldDoc;
-import com.sun.javadoc.RootDoc;
 import com.sun.javadoc.Tag;
-import freemarker.template.Configuration;
-import freemarker.template.DefaultObjectWrapper;
-import freemarker.template.Template;
-import freemarker.template.TemplateException;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.Utils;
@@ -52,7 +47,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     @Override
     public boolean shouldBeProcessed(ClassDoc doc) {
         try {
-            Class type = ResourceBundleExtractorDoclet.getClassForDoc(doc);
+            Class type = HelpUtils.getClassForDoc(doc);
             return JVMUtils.isConcrete(type);
         } catch ( ClassNotFoundException e ) {
             return false;
@@ -98,7 +93,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
         args.put("hidden", new ArrayList<Object>());
         args.put("depreciated", new ArrayList<Object>());
         try {
-            for ( ArgumentSource argumentSource : parsingEngine.extractArgumentSources(ResourceBundleExtractorDoclet.getClassForDoc(classdoc)) ) {
+            for ( ArgumentSource argumentSource : parsingEngine.extractArgumentSources(HelpUtils.getClassForDoc(classdoc)) ) {
                 ArgumentDefinition argDef = argumentSource.createArgumentDefinitions().get(0);
                 FieldDoc fieldDoc = getFieldDoc(classdoc, argumentSource.field.getName());
                 GATKDoc doc = docForArgument(fieldDoc, argDef); // todo -- why can you have multiple ones?
@@ -139,7 +134,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
             if ( fieldDoc.name().equals(name) )
                 return fieldDoc;
 
-            Field field = ResourceBundleExtractorDoclet.getFieldForFieldDoc(fieldDoc);
+            Field field = HelpUtils.getFieldForFieldDoc(fieldDoc);
             if ( field.isAnnotationPresent(ArgumentCollection.class) ) {
                 ClassDoc typeDoc = getRootDoc().classNamed(fieldDoc.type().qualifiedTypeName());
                 if ( typeDoc == null )
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
index dc6e6a533..4527c6afe 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
@@ -1,8 +1,33 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 package org.broadinstitute.sting.utils.help;
 
 import com.sun.javadoc.FieldDoc;
 import com.sun.javadoc.PackageDoc;
 import com.sun.javadoc.ProgramElementDoc;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
 
 import java.lang.reflect.Field;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
index 140e06481..a28a7bcee 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
@@ -28,12 +28,8 @@ package org.broadinstitute.sting.utils.help;
 import com.sun.javadoc.*;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import sun.tools.java.ClassNotFound;
 
 import java.io.*;
-import java.lang.reflect.Field;
 import java.util.*;
 
 /**
@@ -112,7 +108,7 @@ public class ResourceBundleExtractorDoclet {
             if(isRequiredJavadocMissing(currentClass) && isWalker(currentClass))
                 undocumentedWalkers.add(currentClass.name());
 
-            renderHelpText(getClassName(currentClass),currentClass);
+            renderHelpText(HelpUtils.getClassName(currentClass),currentClass);
         }
 
         for(PackageDoc currentPackage: packages)
@@ -177,50 +173,7 @@ public class ResourceBundleExtractorDoclet {
      * @return True if the class of the given name is a walker.  False otherwise.
      */
     protected static boolean isWalker(ClassDoc classDoc) {
-        return assignableToClass(classDoc, Walker.class, true);
-    }
-
-    protected static boolean implementsInterface(ProgramElementDoc classDoc, Class... interfaceClasses) {
-        for ( Class interfaceClass : interfaceClasses )
-            if ( assignableToClass(classDoc, interfaceClass, false) )
-                return true;
-        return false;
-    }
-
-    protected static boolean assignableToClass(ProgramElementDoc classDoc, Class lhsClass, boolean requireConcrete) {
-        try {
-            Class type = getClassForDoc(classDoc);
-            return lhsClass.isAssignableFrom(type) && (! requireConcrete || JVMUtils.isConcrete(type));
-        }
-        catch(Throwable t) {
-            // Ignore errors.
-            return false;
-        }
-    }
-
-    protected static Class getClassForDoc(ProgramElementDoc doc) throws ClassNotFoundException {
-        return Class.forName(getClassName(doc));
-    }
-
-    protected static Field getFieldForFieldDoc(FieldDoc fieldDoc) {
-        try {
-            Class clazz = getClassForDoc(fieldDoc.containingClass());
-            return JVMUtils.findField(clazz, fieldDoc.name());
-        } catch ( ClassNotFoundException e ) {
-            throw new RuntimeException(e);
-        }
-    }
-
-    /**
-     * Reconstitute the class name from the given class JavaDoc object.
-     * @param doc the Javadoc model for the given class.
-     * @return The (string) class name of the given class.
-     */
-    protected static String getClassName(ProgramElementDoc doc) {
-        PackageDoc containingPackage = doc.containingPackage();
-        return containingPackage.name().length() > 0 ?
-                String.format("%s.%s",containingPackage.name(),doc.name()) :
-                String.format("%s",doc.name());
+        return HelpUtils.assignableToClass(classDoc, Walker.class, true);
     }
 
     /**
diff --git a/settings/helpTemplates/generic.index.template.html b/settings/helpTemplates/generic.index.template.html
index 83020a6e0..b494dc582 100644
--- a/settings/helpTemplates/generic.index.template.html
+++ b/settings/helpTemplates/generic.index.template.html
@@ -1,12 +1,15 @@
 <#macro emitGroup group>
   <table border="1" cellpadding="2">
-  <h2>${group}</h2>
+  <h2>${group.name}</h2>
+  <p>
+  ${group.summary}  
+  <p>
   <tr>
      <th>Name</th>
      <th>Summary</th>
   </tr>
     <#list data as datum>
-        <#if datum.group == group>
+        <#if datum.group == group.name>
             <tr>
                <td><a href="${datum.filename}">${datum.name}</a></td>
                <td>${datum.summary}</td>
@@ -21,7 +24,7 @@
   <title>GATK documentation index</title>
 </head>
 <body>
-  <h1>GATK documentation index<h1>
+  <h1>GATK documentation index</h1>
   <#list groups as group>
     <@emitGroup group=group/>
   </#list>