diff --git a/pom.xml b/pom.xml
index 6b3703c89..9d15a0ef2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -754,19 +754,7 @@
                             <useStandardDocletOptions>false</useStandardDocletOptions>
                             <quiet>true</quiet>
                             <show>private</show>
-                            <!--
-                            TODO: Stop GATKDoclet from hardcoding paths and start using parameters.
-                            For now... just run from the base directory, target/site/../..
-                            -->
-                            <destDir>../..</destDir>
-                            <additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden}</additionalparam>
-                            <!--
-                            TODO: Leaving this true applies a patch to the git commited file
-                            TODO: private/resources/clover/api/index.html
-                            TODO: Determine if this file was generated and shoudldn't be touched,
-                            TODO: or patch the file and commit a new version.
-                            -->
-                            <applyJavadocSecurityFix>false</applyJavadocSecurityFix>
+                            <additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${sting.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs</additionalparam>
                         </configuration>
                     </reportSet>
                 </reportSets>
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/PluginManager.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/PluginManager.java
index de071fa7b..38bd9bdcc 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/PluginManager.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/PluginManager.java
@@ -154,17 +154,6 @@ public class PluginManager<PluginType> {
         @SuppressWarnings("unchecked")
         Set<Class<? extends PluginType>> allTypes = reflections.getSubTypesOf(pluginType);
         for( Class<? extends PluginType> type: allTypes ) {
-            // Depending on the root directories/URLs fed to org.reflections, the scanner may pick up classes that are
-            // NOT actually in the classpath. When this happens, Class.forName() returns null, and the allTypes ends up
-            // containing null elements.
-            // This happens for example when the gatkdocs generator is invoked from the root of the source tree.
-            // In this case, ignore the null types, as they were most likely NOT supposed to be scanned, and continue.
-            // TODO: Fix location that the GATKDocs scans, since it currently runs from the source code root, due to
-            // TODO: hardcoded paths!
-
-            if (type == null)
-                continue;
-
             // The plugin manager does not support anonymous classes; to be a plugin, a class must have a name.
             if(JVMUtils.isAnonymous(type))
                 continue;