diff --git a/build.xml b/build.xml
index b93b0d200..416fce4bd 100644
--- a/build.xml
+++ b/build.xml
@@ -318,33 +318,57 @@
                 <striplinebreaks/>
             </filterchain>
         </loadfile>
+
+        <!-- This fileset will contain only source files modified since the resource file was last generated,
+             or all source files if the resource file doesn't exist -->
+        <fileset dir="${basedir}" id="modified.source.files">
+            <include name="${java.source.dir}/**/*.java"/>
+            <include name="${external.dir}/**/*.java"/>
+            <depend targetdir="${basedir}">
+                <mapper type="merge" to="${resource.path}"/>
+            </depend>
+        </fileset>
+
+        <!-- Set the sources.modified property only if our fileset of modified source files is non-empty -->
+        <pathconvert refid="modified.source.files" property="sources.modified" setonempty="false"/>
+
+        <!-- Due to a limitation in the doclet API, we always need to pass package-info files to javadoc -->
+        <fileset dir="${basedir}" id="package.info.files">
+            <include name="${java.source.dir}/**/package-info.java"/>
+            <include name="${external.dir}/**/package-info.java"/>
+        </fileset>
+
         <condition property="uptodate.extracthelp">
             <or>
                 <isset property="disable.help"/>
                 <and>
-                    <uptodate targetfile="${basedir}/${resource.path}">
-                        <srcfiles refid="java.class.files"/>
-                    </uptodate>
-                    <equals arg1="${properties.version}" arg2="${build.version}" />
+                    <not>
+                        <isset property="sources.modified"/>
+                    </not>
+                    <equals arg1="${properties.version}" arg2="${build.version}"/>
                 </and>
             </or>
         </condition>
     </target>
 
-    <target name="extracthelp" depends="init.extracthelp"
-	    description="Extract help key/value pair file from the JavaDoc tags."
-	    unless="uptodate.extracthelp">
+    <target name="extracthelp" depends="init.extracthelp" unless="uptodate.extracthelp"
+	        description="Extract help key/value pair file from the JavaDoc tags.">
         <path id="doclet.classpath">
-          <path refid="external.dependencies" />
-          <pathelement location="${java.classes}" />
+            <path refid="external.dependencies" />
+            <pathelement location="${java.classes}" />
         </path>
 
         <javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
                  docletpathref="doclet.classpath"
                  classpathref="external.dependencies"
+                 classpath="${java.classes}"
                  additionalparam="-build-timestamp &quot;${build.timestamp}&quot; -version-suffix .${build.version} -out ${basedir}/${resource.path} -quiet">
-            <sourcepath path="${java.source.dir}"/>
-            <sourcepath path="${external.dir}"/>
+            <sourcefiles>
+                <union>
+                    <fileset refid="modified.source.files"/>
+                    <fileset refid="package.info.files"/>
+                </union>
+            </sourcefiles>
         </javadoc>
     </target>
 
diff --git a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
index 49a93148b..84b0942e5 100644
--- a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
+++ b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
@@ -27,9 +27,8 @@ package org.broadinstitute.sting.utils.help;
 
 import com.sun.javadoc.*;
 
+import java.io.*;
 import java.util.*;
-import java.io.PrintStream;
-import java.io.IOException;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
@@ -70,8 +69,10 @@ public class ResourceBundleExtractorDoclet {
         String buildTimestamp = null, versionPrefix = null, versionSuffix = null;
 
         for(String[] options: rootDoc.options()) {
-            if(options[0].equals("-out"))
+            if(options[0].equals("-out")) {
+                loadExistingResourceFile(options[1], rootDoc);
                 out = new PrintStream(options[1]);
+            }
             if(options[0].equals("-build-timestamp"))
                 buildTimestamp = options[1];
             if(options[0].equals("-version-prefix"))
@@ -122,6 +123,31 @@ public class ResourceBundleExtractorDoclet {
         return 0;
     }
 
+    /**
+     * Attempts to load the contents of the resource file named by resourceFileName into
+     * our in-memory resource collection resourceText. If the resource file doesn't exist,
+     * prints a notice to the user but does not throw an exception back to the calling method,
+     * since we'll just create a new resource file from scratch in that case.
+     * @param  resourceFileName  name of the resource file to attempt to load.
+     * @param  rootDoc           the documentation root.
+     * @throws IOException       if there is an I/O-related error other than FileNotFoundException
+     *                           while attempting to read the resource file.
+     */
+    private static void loadExistingResourceFile( String resourceFileName, RootDoc rootDoc ) throws IOException {
+        try {
+            BufferedReader resourceFile = new BufferedReader(new FileReader(resourceFileName));
+            try {
+                resourceText.load(resourceFile);
+            }
+            finally {
+                resourceFile.close();
+            }
+        }
+        catch ( FileNotFoundException e ) {
+            rootDoc.printNotice("Resource file not found -- generating a new one from scratch.");
+        }
+    }
+
     /**
      * Determine whether a given class is a walker.
      * @param classDoc the type of the given class.