diff --git a/build.xml b/build.xml
index 2cd8dec03..c468d88fd 100644
--- a/build.xml
+++ b/build.xml
@@ -4,6 +4,7 @@
 
     <property name="build.dir" value="build" />
     <property name="dist.dir" value="dist" />
+    <property name="external.dir" value="external" />
     <property name="java.source.dir" value="java/src" />
     <property name="java.classes" value="${build.dir}/java/classes" />
     <property name="resource.file" value="StingText.properties" />
@@ -33,13 +34,19 @@
 
     <property environment="env"/>
 
-    <dirset id="java.source.files" dir="${java.source.dir}">
-      <patternset>
-	<include name="org/broadinstitute/sting/**"/>
-	<exclude name="**/playground/**" unless="include.playground" />
-	<exclude name="**/oneoffprojects/**" unless="include.oneoffs" />
-      </patternset>
-    </dirset>
+    <patternset id="java.source.pattern">
+        <include name="**/*.java"/>
+        <exclude name="**/playground/**" unless="include.playground" />
+        <exclude name="**/oneoffprojects/**" unless="include.oneoffs" />
+    </patternset>
+
+    <fileset id="java.source.files" dir="${java.source.dir}">
+        <patternset refid="java.source.pattern" />
+    </fileset>
+
+    <fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
+        <patternset refid="java.source.pattern" />
+    </fileset>
 
     <!-- the path for resources that need to go into the GATK jar;
          any additional resources should go into this set. -->
@@ -195,12 +202,28 @@
 
     <target name="gatk.compile" depends="tribble,init,resolve"
             description="compile the source">
-      <!-- Compile the java code from ${src} into build -->
-      <javac srcdir="${java.source.dir}" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies">
-          <exclude name="**/examples/**" />
-        <exclude name="**/playground/**" unless="include.playground"/>
-        <exclude name="**/oneoffprojects/**" unless="include.oneoffs"/>
-      </javac>
+        <!-- Compile the java code from ${src} into build -->
+        <javac srcdir="${java.source.dir}" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies">
+            <exclude name="**/examples/**" />
+            <exclude name="**/playground/**" unless="include.playground"/>
+            <exclude name="**/oneoffprojects/**" unless="include.oneoffs"/>
+        </javac>
+
+        <pathconvert property="external.build.dir">
+            <path path="${java.classes}"/>
+        </pathconvert>
+
+        <!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
+        <pathconvert property="external.gatk.classpath">
+            <path path="${java.classes}"/>
+            <path refid="external.dependencies" />
+        </pathconvert>
+
+        <subant target="compile" genericantfile="build.xml">
+            <property name="build.dir" value="${external.build.dir}" />
+            <property name="gatk.classpath" value="${external.gatk.classpath}" />
+            <fileset dir="${basedir}" includes="external/*/build.xml" />
+        </subant>
     </target>
 
     <!-- Queue depends on the gatk since it contains the StingUtils (including CommandLine) -->
@@ -239,11 +262,13 @@
           <path refid="external.dependencies" />
           <pathelement location="${java.classes}" />
         </path>
+
       <javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
 	       docletpathref="doclet.classpath"
 	       classpathref="external.dependencies"
-	       additionalparam="-build-timestamp &quot;${build.timestamp}&quot; -version-suffix .${build.version} -out ${basedir}/${resource.path}">
-	<packageset refid="java.source.files"/>
+	       additionalparam="-build-timestamp &quot;${build.timestamp}&quot; -version-suffix .${build.version} -out ${basedir}/${resource.path} -quiet">
+	    <fileset refid="java.source.files"/>
+        <fileset refid="external.source.files"/>
       </javadoc>
     </target>
 
@@ -611,7 +636,7 @@
       <mkdir dir="${dist.dir}/packages" />
       <xslt in="packages/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="packages/CreatePackager.xsl" />
       <ant antfile="${dist.dir}/packages/BuildPicardPrivate.xml">
-	<property name="additional.jars" value="${required.picard.jars}" />
+	    <property name="additional.jars" value="${required.picard.jars}" />
       </ant>
     </target>
 
@@ -619,7 +644,7 @@
     <!-- Find bug tasks                                                                   -->
     <!-- ******************************************************************************** -->
     <path id="findbugs.classpath">
-            <fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
+      <fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
     </path>
     <target         name="findbugs" depends="dist">
         <antcall    target  ="resolve">
@@ -639,9 +664,7 @@
          <sourcePath    path="../java/src" />
          <class         location="dist/GenomeAnalysisTK.jar" />
        </findbugs>
-     </target>
-
-
+    </target>
 
     <target name="clean" description="clean up" depends="tribble.clean,clean.javadoc">
         <delete dir="out"/>
@@ -651,6 +674,5 @@
         <delete dir="${dist.dir}"/>
         <!-- When we clean, make sure to clean out tribble as well -->
         <ant antfile="tribble/build.xml" target="clean"/>
-
     </target>
 </project>
diff --git a/java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java b/java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java
deleted file mode 100644
index cad8638e6..000000000
--- a/java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * Copyright (c) 2009 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.
- */
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.commandline.Output;
-
-import java.io.PrintStream;
-
-/**
- * An example walker for illustrative purposes.
- */
-public class HelloWalker extends LocusWalker<Integer,Long> {
-    @Output
-    PrintStream out;
-
-    /**
-     * The map function runs once per single-base locus, and accepts a 'context', a
-     * data structure consisting of the reads which overlap the locus, the sites over
-     * which they fall, and the base from the reference that overlaps.
-     * @param tracker The accessor for reference metadata.
-     * @param ref The reference base that lines up with this locus.
-     * @param context Information about reads aligning to this locus.
-     * @return In this case, returns a count of how many loci were seen at this site (1).
-     */
-    @Override
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        out.printf("Hello locus %s; your ref base is %c and you have %d reads%n", context.getLocation(), ref.getBase(), context.getBasePileup().size() );
-        return 1;
-    }
-
-    /**
-     * Provides an initial value for the reduce function.  Hello walker counts loci,
-     * so the base case for the inductive step is 0, indicating that the walker has seen 0 loci.
-     * @return 0.
-     */
-    @Override
-    public Long reduceInit() { return 0L; }
-
-    /**
-     * Combines the result of the latest map with the accumulator.  In inductive terms,
-     * this represents the step loci[x + 1] = loci[x] + 1
-     * @param value result of the map.
-     * @param sum accumulator for the reduce.
-     * @return The total count of loci processed so far.
-     */
-    @Override
-    public Long reduce(Integer value, Long sum) {
-        return sum + value;
-    }
-
-    /**
-     * Retrieves the final result of the traversal.
-     * @param result The ultimate value of the traversal, produced when map[n] is combined with reduce[n-1]
-     *               by the reduce function. 
-     */
-    @Override
-    public void onTraversalDone(Long result) {
-        out.println("Number of loci viewed is: " + result);
-    }
-}
diff --git a/java/src/org/broadinstitute/sting/gatk/examples/build.xml b/java/src/org/broadinstitute/sting/gatk/examples/build.xml
deleted file mode 100644
index 8acab9eac..000000000
--- a/java/src/org/broadinstitute/sting/gatk/examples/build.xml
+++ /dev/null
@@ -1,40 +0,0 @@
-<!--
-  ~ Copyright (c) 2009 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.
-  -->
-
-<project name="BuildHelloWalker" default="dist" basedir=".">
-    <description>Build the GATK examples</description>
-    
-    <property name="gatk.home" value="${user.home}/GenomeAnalysisTK" />
-    <property name="walker.home" value="${gatk.home}/walkers" />
-
-    <target name="dist">
-      <mkdir dir="${walker.home}" />
-      <javac srcdir="${basedir}" destdir="${walker.home}">
-          <classpath>
-            <fileset dir="${gatk.home}" includes="GenomeAnalysisTK.jar" />
-          </classpath>
-      </javac>
-    </target>
-
-</project>