diff --git a/core/ConnectionHelper.inc b/api/ConnectionHelper.inc
similarity index 99%
rename from core/ConnectionHelper.inc
rename to api/ConnectionHelper.inc
index 59f811e2..02db7e7f 100644
--- a/core/ConnectionHelper.inc
+++ b/api/ConnectionHelper.inc
@@ -1,7 +1,5 @@
 <?php
 
-
-
 /**
  * @file 
  * Connection Helper Class
diff --git a/core/MimeClass.inc b/api/MimeClass.inc
similarity index 100%
rename from core/MimeClass.inc
rename to api/MimeClass.inc
diff --git a/core/ObjectHelper.inc b/api/ObjectHelper.inc
similarity index 97%
rename from core/ObjectHelper.inc
rename to api/ObjectHelper.inc
index 70f73d4b..2d844a97 100644
--- a/core/ObjectHelper.inc
+++ b/api/ObjectHelper.inc
@@ -33,7 +33,7 @@ class ObjectHelper {
    */
   function ObjectHelper() {
     drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
-    module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
     $connectionHelper = new ConnectionHelper();
     //$this->fedoraUser = $connectionHelper->getUser();
     //$this->fedoraPass = $connectionHelper->getPassword();
@@ -56,7 +56,7 @@ class ObjectHelper {
    */
   function makeObject($pid, $dsID, $asAttachment = FALSE, $label = NULL, $filePath=FALSE, $version=NULL, $forceSoap = TRUE) {
     global $user;
-    module_load_include('inc', 'fedora_repository', 'ContentModel');
+    module_load_include('inc', 'fedora_repository', 'core/ContentModel');
     if ($pid == NULL || $dsID == NULL) {
       drupal_set_message(t("no pid or dsid given to create an object with"), 'error');
       return ' ';
@@ -176,7 +176,7 @@ class ObjectHelper {
            * for the mimetype in question.
            */
           if ($pos === FALSE) {
-            module_load_include('inc', 'fedora_repository', 'MimeClass');
+            module_load_include('inc', 'fedora_repository', 'api/MimeClass');
             $mimeclass = new MimeClass();
             $ext = $mimeclass->get_extension($mimeType);
             $suggestedFileName = "$label.$ext";
@@ -207,7 +207,7 @@ class ObjectHelper {
    * @return type 
    */
   function getCollectionInfo($pid, $query = NULL) {
-    module_load_include('inc', 'fedora_repository', 'CollectionClass');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
     $collectionClass = new CollectionClass();
     $results = $collectionClass->getRelatedItems($pid, $query);
     return $results;
@@ -360,7 +360,7 @@ class ObjectHelper {
   function getFormattedDC($item) {
     global $base_url;
     $path = drupal_get_path('module', 'fedora_repository');
-    module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
 
     $dsid = array_key_exists('QDC', $item->get_datastreams_list_as_array()) ? 'QDC' : 'DC';
     $xmlstr = $item->get_datastream_dissemination($dsid);
@@ -440,10 +440,10 @@ class ObjectHelper {
    */
   function get_formatted_datastream_list($object_pid, $contentModels, &$fedoraItem) {
     global $fedoraUser, $fedoraPass, $base_url, $user;
-    module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
-    module_load_include('inc', 'fedora_repository', 'ContentModel');
+    module_load_include('inc', 'fedora_repository', 'core/ContentModel');
 
     $path = drupal_get_path('module', 'fedora_repository');
     $dataStreamBody = '';
@@ -514,7 +514,7 @@ class ObjectHelper {
    *
    */
   function getStream($pid, $dsid, $showError = FALSE) {
-    module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
     $soapHelper = new ConnectionHelper();
     try {
       $client = $soapHelper->getSoapClient(variable_get('fedora_soap_url', 'http://localhost:8080/fedora/services/access?wsdl'));
@@ -548,7 +548,7 @@ class ObjectHelper {
    * @return array 
    */
   function get_content_models_list($pid, $include_fedora_system_content_models = FALSE) {
-    module_load_include('inc', 'fedora_repository', 'CollectionClass');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
     $collectionHelper = new CollectionClass();
     $pids = array();
     $query = 'select $object from <#ri>
@@ -665,7 +665,7 @@ class ObjectHelper {
     //show the collections datastreams
     if ($results->length > 0 || $isCollection == TRUE) {
       //  if(strlen($objectList)>22||$contentModel=='Collection'||$contentModel=='Community')//length of empty dom still equals 22 because of <table/> etc
-      module_load_include('inc', 'Fedora_Repository', 'CollectionPolicy');
+      module_load_include('inc', 'fedora_repository', 'core/CollectionPolicy');
       $collectionPolicyExists = $objectHelper->getMimeType($pid, CollectionPolicy::getDefaultDSID());
       if (user_access(ObjectHelper :: $INGEST_FEDORA_OBJECTS) && $collectionPolicyExists) {
         if (!empty($collectionPolicyExists)) {
@@ -790,7 +790,7 @@ class ObjectHelper {
       return NULL;
     }
     $output = '';
-    module_load_include('inc', 'fedora_repository', 'ContentModel');
+    module_load_include('inc', 'fedora_repository', 'core/ContentModel');
     if (($cm = ContentModel :: loadFromModel($contentModel)) !== FALSE && $cm->validate()) {
       $output .= $cm->displayExtraFieldset($pid, $page_number);
     }
@@ -810,7 +810,7 @@ class ObjectHelper {
       return FALSE;
     }
 
-    module_load_include('inc', 'fedora_repository', 'ContentModel');
+    module_load_include('inc', 'fedora_repository', 'core/ContentModel');
     if ($dsid != NULL && $pid != NULL && ($cm = ContentModel::loadFromObject($pid)) !== FALSE) {
       $cm->execAddDatastreamMethods($dsid, $file);
     }
diff --git a/api/fedora_collection.inc b/api/fedora_collection.inc
index a82bf39b..0f85bdca 100644
--- a/api/fedora_collection.inc
+++ b/api/fedora_collection.inc
@@ -4,7 +4,7 @@
  * @file
  * Operations that affect a Fedora repository at a collection level.
  */
-module_load_include('inc', 'fedora_repository', 'CollectionClass');
+module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
 module_load_include('inc', 'fedora_repository', 'api/fedora_item');
 module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
 module_load_include('module', 'fedora_repository');
@@ -68,7 +68,7 @@ function export_collection($collection_pid, $relationship = 'isMemberOfCollectio
  * @param <type> $query_format R
  */
 function get_related_items_as_xml($collection_pid, $relationship = array('isMemberOfCollection'), $limit = 10000, $offset = 0, $active_objects_only = TRUE, $cmodel = NULL, $orderby = '$title') {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
 
   global $user;
   if (!fedora_repository_access(OBJECTHELPER :: $OBJECT_HELPER_VIEW_FEDORA, $pid, $user)) {
diff --git a/api/fedora_export.inc b/api/fedora_export.inc
index f3c82160..f5a6a7b4 100644
--- a/api/fedora_export.inc
+++ b/api/fedora_export.inc
@@ -85,7 +85,7 @@ function export_objects_for_pid($pid, $dir, &$log) {
  * @return type 
  */
 function export_foxml_for_pid($pid, $dir, $paths, &$log, $format = FOXML_11, $remove_islandora = FALSE) {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   $ob_helper = new ObjectHelper();
   if (!$object_xml = $ob_helper->getObject($pid, 'migrate', $format)) {
     $log[] = log_line(t("Failed to get foxml for %pid", array('%pid' => $pid)), 'error');
diff --git a/api/fedora_imageapi.module b/api/fedora_imageapi.module
index 99c2cfd2..0d92c6f2 100644
--- a/api/fedora_imageapi.module
+++ b/api/fedora_imageapi.module
@@ -24,7 +24,7 @@ function fedora_imageapi_menu() {
  * @param string $params
  */
 function fedora_repository_image_manip($pid = '', $dsid = '', $op = '', $params = '') {
-  module_load_include('inc', 'Fedora_Repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   module_load_include('module', 'imageapi');
   $obj = new ObjectHelper();
   $mimetype = $obj->getMimeType($pid, $dsid);
diff --git a/api/fedora_item.inc b/api/fedora_item.inc
index 54a9158b..2edfd285 100644
--- a/api/fedora_item.inc
+++ b/api/fedora_item.inc
@@ -28,7 +28,7 @@ class Fedora_Item {
    */
   function __construct($pid) {
     drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
-    module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
     module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
 
     $this->pid = $pid;
@@ -75,7 +75,7 @@ class Fedora_Item {
    * @return type 
    */
   function add_datastream_from_file($datastream_file, $datastream_id, $datastream_label = NULL, $datastream_mimetype = '', $controlGroup = 'M', $logMessage = NULL) {
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     if (!is_file($datastream_file)) {
       drupal_set_message("$datastream_file not found<br />", 'warning');
       return;
@@ -848,7 +848,7 @@ class Fedora_Item {
    */
   static function soap_call($function_name, $params_array, $quiet = FALSE) {
     if (!self::$connection_helper) {
-      module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
+      module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
       self::$connection_helper = new ConnectionHelper();
     }
     switch ($function_name) {
diff --git a/core/BatchIngest.inc b/core/BatchIngest.inc
index c78be313..b8f75183 100644
--- a/core/BatchIngest.inc
+++ b/core/BatchIngest.inc
@@ -9,7 +9,7 @@
  */
 function batch_creation_form(&$form_state, $collection_pid, $content_models) {
   module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
-  module_load_include('inc', 'fedora_repository', 'CollectionPolicy');
+  module_load_include('inc', 'fedora_repository', 'core/CollectionPolicy');
   $cm_options = array();
   $name_mappings = array();
   foreach ($content_models as $content_model) {
@@ -86,7 +86,7 @@ function batch_creation_form_validate($form, &$form_state) {
 }
 
 function batch_creation_form_submit($form, &$form_state) {
-  module_load_include('inc', 'fedora_repository', 'ContentModel');
+  module_load_include('inc', 'fedora_repository', 'core/ContentModel');
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   global $user;
   $namespace_mappings = array();
@@ -163,8 +163,8 @@ function batch_creation_form_submit($form, &$form_state) {
  * @param <string> $metadata
  */
 function create_batch_objects($label, $content_model, $object_files, $collection_pid, $namespace, $metadata) {
-  module_load_include('inc', 'fedora_repository', 'ContentModel');
-  module_load_include('inc', 'fedora_repository', 'MimeClass');
+  module_load_include('inc', 'fedora_repository', 'core/ContentModel');
+  module_load_include('inc', 'fedora_repository', 'api/MimeClass');
   module_load_include('inc', 'fedora_reppository', 'api/fedora_item');
 
   $cm = ContentModel::loadFromModel($content_model, 'ISLANDORACM');
@@ -219,8 +219,8 @@ function create_batch_objects($label, $content_model, $object_files, $collection
  */
 function batch_create_dc_from_mods($mods_xml) {
   $path = drupal_get_path('module', 'fedora_repository');
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
-  module_load_include('inc', 'fedora_repository', 'CollectionClass');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
 
   if ($xmlstr == NULL || strlen($xmlstr) < 5) {
     return " ";
diff --git a/core/CollectionClass.inc b/core/CollectionClass.inc
index 82e4739e..397a4a9d 100644
--- a/core/CollectionClass.inc
+++ b/core/CollectionClass.inc
@@ -29,7 +29,7 @@ class CollectionClass {
    */
   function __construct($pid = NULL) {
     if (!empty($pid)) {
-      module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+      module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
       $this->collectionObject = new ObjectHelper($pid);
       $this->pid = $pid;
     }
@@ -45,7 +45,7 @@ class CollectionClass {
    * @return type 
    */
   function getRelatedObjects($pid, $limit, $offset, $itqlquery=NULL) {
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     $objectHelper = new ObjectHelper();
     if (!isset($itqlquery)) {
       // $query_string = $objectHelper->getStream($pid, 'QUERY', 0);
@@ -65,7 +65,7 @@ class CollectionClass {
    * @return type 
    */
   function getRelatedItems($pid, $itqlquery = NULL, $limit = NULL, $offset = NULL) {
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
     if (!isset($limit)) {
       $limit = 1000;
@@ -193,7 +193,7 @@ class CollectionClass {
    * @return ContentModel 
    */
   function getContentModels($collection_pid, $showError = TRUE) {
-    module_load_include('inc', 'Fedora_Repository', 'ContentModel');
+    module_load_include('inc', 'fedora_repository', 'core/ContentModel');
     $collection_stream = $this->getCollectionPolicyStream($collection_pid);
     try {
       $xml = new SimpleXMLElement($collection_stream);
@@ -220,7 +220,7 @@ class CollectionClass {
    * $dsid is the datastream id of the content model.
    */
   function getNextPid($pid, $dsid) {
-    module_load_include('inc', 'Fedora_Repository', 'ConnectionHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
     $pidNameSpace = $this->getPidNameSpace($pid, $dsid);
     $pname = substr($pidNameSpace, 0, strpos($pidNameSpace, ":"));
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
@@ -437,7 +437,7 @@ class CollectionClass {
       'name' => variable_get('fedora_admin_user', 'fedoraAdmin')
     );
     $admin_user = user_load($username);
-    module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
     $connectionHelper = new ConnectionHelper();
     try {
       $soapClient = $connectionHelper->getSoapClient(variable_get('fedora_soap_manage_url', 'http://localhost:8080/fedora/services/management?wsdl'));
@@ -480,7 +480,7 @@ class CollectionClass {
    * @return type 
    */
   function getXslContent($pid, $path, $canUseDefault = TRUE) {
-    module_load_include('inc', 'fedora_repository', 'CollectionClass');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
     $collectionClass = new CollectionClass();
     $xslContent = $collectionClass->getCollectionViewStream($pid);
     if (!$xslContent && $canUseDefault) { //no xslt so we will use the default sent with the module
@@ -577,7 +577,7 @@ class CollectionClass {
   function getIngestInterface() {
     global $base_url;
     $objectHelper = new ObjectHelper();
-    module_load_include('inc', 'Fedora_Repository', 'CollectionPolicy');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionPolicy');
     $collectionPolicyExists = $objectHelper->getMimeType($this->pid, CollectionPolicy::getDefaultDSID());
     if (user_access(ObjectHelper :: $INGEST_FEDORA_OBJECTS) && $collectionPolicyExists) {
       if (!empty($collectionPolicyExists)) {
diff --git a/core/CollectionManagement.inc b/core/CollectionManagement.inc
index 39d33456..d52d479d 100644
--- a/core/CollectionManagement.inc
+++ b/core/CollectionManagement.inc
@@ -21,7 +21,7 @@ function collection_management_form(&$form_state, $this_collection_pid, $content
     }
   }
   module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
-  module_load_include('inc', 'fedora_repository', 'CollectionPolicy');
+  module_load_include('inc', 'fedora_repository', 'core/CollectionPolicy');
   $item = new Fedora_Item($this_collection_pid);
   $collection_name = $item->objectProfile->objLabel;
   $new_content_models = get_content_models_as_option_array();
diff --git a/core/CollectionPolicy.inc b/core/CollectionPolicy.inc
index be9e7a92..e94d5036 100644
--- a/core/CollectionPolicy.inc
+++ b/core/CollectionPolicy.inc
@@ -4,7 +4,7 @@
  * @file 
  * Collection Policy Class
  */
-module_load_include('inc', 'fedora_repository', 'XMLDatastream');
+module_load_include('inc', 'fedora_repository', 'core/XMLDatastream');
 
 /**
  * Collection Policy class ??
@@ -137,7 +137,7 @@ class CollectionPolicy extends XMLDatastream {
   public static function ingestBlankPolicy($pid, $name, $policyDsid, $model_pid, $model_namespace, $relationship, $searchField, $searchValue) {
     $ret = FALSE;
     if (($cp = self::loadFromCollection($pid)) === FALSE) {   //removed second, non-existant variable
-      module_load_include('inc', 'fedora_repository', 'ContentModel');
+      module_load_include('inc', 'fedora_repository', 'core/ContentModel');
       if (($cm = ContentModel::loadFromModel($model_pid)) !== FALSE && $cm->validate()) {
         $newDom = new DOMDocument('1.0', 'utf-8');
         $newDom->formatOutput = TRUE;
@@ -387,7 +387,7 @@ class CollectionPolicy extends XMLDatastream {
   function getContentModels() {
     $ret = FALSE;
     if ($this->validate()) {
-      module_load_include('inc', 'Fedora_Repository', 'ContentModel');
+      module_load_include('inc', 'fedora_repository', 'core/ContentModel');
       $ret = array();
       $content_models = $this->xml->getElementsByTagName('content_models')->item(0)->getElementsByTagName('content_model');
       for ($i = 0; $i < $content_models->length; $i++) {
diff --git a/core/ContentModel.inc b/core/ContentModel.inc
index cbacd422..0b232eea 100644
--- a/core/ContentModel.inc
+++ b/core/ContentModel.inc
@@ -8,7 +8,7 @@
  * @file 
  * Content Model Class
  */
-module_load_include('inc', 'fedora_repository', 'XMLDatastream');
+module_load_include('inc', 'fedora_repository', 'core/XMLDatastream');
 
 /**
  * Conent Model ??
@@ -41,7 +41,7 @@ class ContentModel extends XMLDatastream {
   public static function loadFromObject($pid) {
     $ret = FALSE;
     if (self::valid_pid($pid)) {
-      module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+      module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
       $objectHelper = new ObjectHelper();
 
       $content_models = $objectHelper->get_content_models_list($pid);
@@ -436,7 +436,7 @@ class ContentModel extends XMLDatastream {
    and $object <fedora-model:state> <info:fedora/fedora-system:def/model#Active>)
    order by $title';
 
-    module_load_include('inc', 'fedora_repository', 'CollectionClass');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
 
     $collectionHelper = new CollectionClass();
     $xml = simplexml_load_string($collectionHelper->getRelatedItems($this->pid, $query));
@@ -1177,7 +1177,7 @@ class ContentModel extends XMLDatastream {
       }
       else {
         // Assume DC form if none is specified.
-        module_load_include('inc', 'fedora_repository', 'formClass');
+        module_load_include('inc', 'fedora_repository', 'core/formClass');
         $metaDataForm = new formClass();
         $ret = $metaDataForm->updateMetaData($form_state['values']['form_id'], $form_state['values'], $soap_client);
         $form_state['storage'] = NULL;
diff --git a/core/SearchClass.inc b/core/SearchClass.inc
index 751dbbfa..fd15de40 100644
--- a/core/SearchClass.inc
+++ b/core/SearchClass.inc
@@ -185,7 +185,7 @@ class SearchClass {
    * @return type 
    */
   function quickSearch($type, $query, $showForm = 1, $orderBy = 0, & $userArray) {
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
     if (user_access('view fedora collection')) {
       $numberOfHistPerPage = '5000'; //hack for IR they do not want next button
@@ -237,7 +237,7 @@ class SearchClass {
    * @return type 
    */
   function getTerms($fieldName, $startTerm, $displayName = NULL) {
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
     $indexName = variable_get('fedora_index_name', 'DemoOnLucene');
     $searchUrl = variable_get('fedora_fgsearch_url', 'http://localhost:8080/fedoragsearch/rest');
@@ -269,7 +269,7 @@ class SearchClass {
    * @return type 
    */
   function custom_search($query, $startPage=1, $xslt= '/xsl/advanced_search_results.xsl', $numberOfHistPerPage = 50) {
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
 
     if (user_access('view fedora collection')) {
diff --git a/core/SecurityClass.inc b/core/SecurityClass.inc
index 1e2b1835..e02ef6c8 100644
--- a/core/SecurityClass.inc
+++ b/core/SecurityClass.inc
@@ -30,7 +30,7 @@ class SecurityClass {
    */
   function canIngestHere($collection_pid) {
     global $user;
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     $objectHelper = new ObjectHelper();
     // get the childsecurity policy from the collection.
     $policyStream = $objectHelper->getStream($collection_pid, SECURITYCLASS :: $SECURITY_CLASS_SECURITY_STREAM, FALSE);
diff --git a/core/formClass.inc b/core/formClass.inc
index be5ef9d2..48cc0ef7 100644
--- a/core/formClass.inc
+++ b/core/formClass.inc
@@ -206,7 +206,7 @@ class formClass {
       return;
     }
     module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     $form = array();
     $form['fedora_repository_name'] = array(
       '#type' => 'textfield',
@@ -523,7 +523,7 @@ class formClass {
    * @return array
    */
   function createQDCIngestFormPageTwo($collection_pid, $collection_label, array &$form_state) {
-    module_load_include('inc', 'fedora_repository', 'ContentModel');
+    module_load_include('inc', 'fedora_repository', 'core/ContentModel');
     $form = array();
     $content_model_pid = ContentModel::getPidFromIdentifier($form_state['values']['models']);
     $content_model_dsid = ContentModel::getDSIDFromIdentifier($form_state['values']['models']);
@@ -558,7 +558,7 @@ class formClass {
    * @return array
    */
   function createQDCIngestForm($collection_pid, $collection_label, array &$form_state) {
-    module_load_include('inc', 'fedora_repository', 'CollectionPolicy');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionPolicy');
     $form_state['storage']['step'] = empty($form_state['storage']['step']) ? 1 : $form_state['storage']['step'];
     if ($form_state['storage']['step'] == 1) {
       return $this->createQDCIngestFormPageOne($collection_pid, $collection_label, $form_state);
@@ -603,8 +603,8 @@ class formClass {
     //dump_vars($form_state);
     // Populate the list of datastream IDs.
 
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
-    module_load_include('inc', 'fedora_repository', 'ContentModel');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'core/ContentModel');
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
 
     $obj_helper = new ObjectHelper();
diff --git a/fedora_repository.module b/fedora_repository.module
index 56859edb..989c6290 100644
--- a/fedora_repository.module
+++ b/fedora_repository.module
@@ -8,7 +8,7 @@
  * the name and pid can also be passed as url parameters
  */
 function fedora_repository_admin() {
-  module_load_include('inc', 'fedora_repository', 'formClass');
+  module_load_include('inc', 'fedora_repository', 'core/formClass');
   $adminForm = new formClass();
   return $adminForm->createAdminForm();
 }
@@ -18,7 +18,7 @@ function fedora_repository_admin() {
  * calls the fedora_repositorys_admin form
  */
 function fedora_repository_menu() {
-  module_load_include('inc', 'fedora_repository', 'formClass');
+  module_load_include('inc', 'fedora_repository', 'core/formClass');
   $adminMenu = new formClass();
   return $adminMenu->createMenu();
 }
@@ -72,7 +72,7 @@ function fedora_repository_purge_object($pid = NULL, $name = NULL) {
  * @return type 
  */
 function fedora_repository_collection_view($pid = NULL, $collection = NULL, $pageNumber = NULL) {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   global $user;
   if (!fedora_repository_access(OBJECTHELPER :: $OBJECT_HELPER_VIEW_FEDORA, $pid, $user)) {
     drupal_set_message(t("You do not have access to Fedora objects within the attempted namespace or access to Fedora denied."), 'error');
@@ -86,7 +86,7 @@ function fedora_repository_collection_view($pid = NULL, $collection = NULL, $pag
 
   $content = '';
 
-  module_load_include('inc', 'fedora_repository', 'CollectionClass');
+  module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
   $collectionClass = new CollectionClass();
   $results = $collectionClass->getRelatedItems($pid, NULL);
   $content .= $objectHelper->parseContent($results, $pid, $dsId, $collection, $pageNumber);
@@ -103,7 +103,7 @@ function fedora_repository_collection_view($pid = NULL, $collection = NULL, $pag
  */
 function fedora_repository_ingest_object($collection_pid=NULL, $collection_label = NULL, $content_model = NULL) {
   module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   if (!user_access('ingest new fedora objects')) {
     drupal_set_message(t('You do not have permission to ingest.'), 'error');
     return '';
@@ -151,9 +151,9 @@ function fedora_repository_ingest_form_submit(array $form, array &$form_state) {
   }
   elseif ($form_state['clicked_button']['#id'] == 'edit-submit') {
     global $base_url;
-    module_load_include('inc', 'fedora_repository', 'CollectionClass');
-    module_load_include('inc', 'fedora_repository', 'CollectionPolicy');
-    module_load_include('inc', 'fedora_repository', 'ContentModel');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionPolicy');
+    module_load_include('inc', 'fedora_repository', 'core/ContentModel');
 
     $contentModelPid = ContentModel::getPidFromIdentifier($form_state['values']['models']);
     $contentModelDsid = ContentModel::getDSIDFromIdentifier($form_state['values']['models']);
@@ -222,8 +222,8 @@ function fedora_repository_ingest_form_validate($form, &$form_state) {
         }
 
         if (isset($form_state['values']['ingest-file-location']) && file_exists($form_state['values']['ingest-file-location'])) {
-          module_load_include('inc', 'fedora_repository', 'ContentModel');
-          module_load_include('inc', 'fedora_repository', 'MimeClass');
+          module_load_include('inc', 'fedora_repository', 'core/ContentModel');
+          module_load_include('inc', 'fedora_repository', 'api/MimeClass');
 
           $file = $form_state['values']['ingest-file-location'];
 
@@ -267,7 +267,7 @@ function fedora_repository_ingest_form_validate($form, &$form_state) {
  * @return type 
  */
 function fedora_repository_ingest_form(&$form_state, $collection_pid, $collection_label = NULL, $content_model = NULL) {
-  module_load_include('inc', 'fedora_repository', 'formClass');
+  module_load_include('inc', 'fedora_repository', 'core/formClass');
 // For the sake of easily maintaining the module in different core versions create our own form_values variable.
   if (empty($form_state['storage']['step'])) {
     $form_state['storage']['step'] = 1;
@@ -367,8 +367,8 @@ function add_stream_form_submit($form, &$form_state) {
     $form_state['rebuild'] = TRUE;
     return;
   }
-  module_load_include('inc', 'fedora_repository', 'MimeClass');
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/MimeClass');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   $pathToModule = drupal_get_path('module', 'fedora_repository');
 
@@ -412,7 +412,7 @@ function add_stream_form_submit($form, &$form_state) {
  * @return type 
  */
 function add_stream_form(&$form_state, $pid) {
-  module_load_include('inc', 'fedora_repository', 'formClass');
+  module_load_include('inc', 'fedora_repository', 'core/formClass');
   $addDataStreamForm = new formClass();
   return $addDataStreamForm->createAddDataStreamForm($pid, $form_state);
 }
@@ -470,7 +470,7 @@ function add_stream_form_validate($form, &$form_state) {
  * @return type 
  */
 function fedora_repository_purge_stream($pid = NULL, $dsId = NULL, $name = NULL) {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   global $user;
   if ($pid == NULL || $dsId == NULL) {
     drupal_set_message(t('You must specify an object pid and DataStream ID to purge a datastream'), 'error');
@@ -495,7 +495,7 @@ function fedora_repository_purge_stream($pid = NULL, $dsId = NULL, $name = NULL)
  * @return type 
  */
 function fedora_repository_purge_object_form_submit($form, &$form_state) {
-  module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
   $pid = $form_state['values']['pid'];
   if (!isset($form_state['storage']['confirm'])) {
     $form_state['storage']['confirm'] = TRUE; // this will cause the form to be rebuilt, entering the confirm part of the form
@@ -609,7 +609,7 @@ function fedora_repository_replace_stream($pid, $dsId, $dsLabel, $collectionName
  */
 function fedora_repository_replace_stream_form(&$form_state, $pid, $dsId, $dsLabel) {
 //module_load_module_load_include('hp', ''Fedora_Repository'', 'config', 'fedora_repository', '');
-  module_load_include('inc', 'Fedora_Repository', 'formClass');
+  module_load_include('inc', 'fedora_repository', 'core/formClass');
 //$client = getSoapClient(variable_get('fedora_soap_manage_url', 'http://localhost:8080/fedora/services/management?wsdl'));
   $replaceDataStreamForm = new formClass();
   return $replaceDataStreamForm->createReplaceDataStreamForm($pid, $dsId, $dsLabel, $form_state);
@@ -635,7 +635,7 @@ function fedora_repository_replace_stream_form_validate($form, &$form_state) {
     }
 
     $doc = new DOMDocument();
-    module_load_include('inc', 'Fedora_Repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     $mime = new MimeClass();
     if ($mime->getType($file->filepath) == 'text/xml' && !$doc->load($file->filepath)) {
       form_set_error('file', 'Invalid XML format.');
@@ -665,7 +665,7 @@ function fedora_repository_replace_stream_form_submit($form, &$form_state) {
     $dsLabel = substr($dsLabel, 0, $indexOfDot);
     $dsLabel .= substr($file->filename, strrpos($file->filename, '.')); // Add the file extention to the end of the label.;
   }
-  module_load_include('inc', 'Fedora_Repository', 'MimeClass');
+  module_load_include('inc', 'fedora_repository', 'api/MimeClass');
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
 
   $file_basename = basename($file->filepath);
@@ -693,7 +693,7 @@ function fedora_repository_replace_stream_form_submit($form, &$form_state) {
  * @return type 
  */
 function fedora_repository_edit_qdc_page($pid = NULL, $dsId = NULL) {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   global $user;
   if ($pid == NULL || $dsId == NULL) {
     drupal_set_message(t('You must specify an object pid and a Dublin Core DataStream ID to edit metadata'), 'error');
@@ -717,8 +717,8 @@ function fedora_repository_edit_qdc_page($pid = NULL, $dsId = NULL) {
  * @return type 
  */
 function fedora_repository_edit_qdc_form(&$form_state, $pid, $dsId = NULL) {
-  module_load_include('inc', 'fedora_repository', 'ContentModel');
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'core/ContentModel');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   if ($pid == NULL) {
     drupal_set_message(t('You must specify an object pid!'), 'error');
   }
@@ -728,8 +728,8 @@ function fedora_repository_edit_qdc_form(&$form_state, $pid, $dsId = NULL) {
     return ' ';
   }
 
-  module_load_include('inc', 'fedora_repository', 'formClass');
-  module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
+  module_load_include('inc', 'fedora_repository', 'core/formClass');
+  module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
   $soapHelper = new ConnectionHelper();
   $client = $soapHelper->getSoapClient(variable_get('fedora_soap_url', 'http://localhost:8080/fedora/services/access?wsdl'));
 // Check if there is a custom edit metadata function defined in the content model.
@@ -787,7 +787,7 @@ function fedora_repository_edit_qdc_form_submit($form, &$form_state) {
     $xml_form->submit($form, $form_state);
   }
   else {
-    module_load_include('inc', 'fedora_repository', 'ConnectionHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ConnectionHelper');
     global $base_url;
     if (strstr($form_state['clicked_button']['#id'], 'edit-submit')) {
 
@@ -797,13 +797,13 @@ function fedora_repository_edit_qdc_form_submit($form, &$form_state) {
 
 // Check the content model for a custom edit metadata form submit function.
       if (isset($form_state['values']['pid'])) {
-        module_load_include('inc', 'fedora_repository', 'ContentModel');
+        module_load_include('inc', 'fedora_repository', 'core/ContentModel');
         if (($cm = ContentModel::loadFromObject($form_state['values']['pid'])) !== FALSE) {
           return $cm->handleEditMetadataForm($form_state['values']['form_id'], $form_state, $client);
         }
       }
 
-      module_load_include('inc', 'fedora_repository', 'formClass');
+      module_load_include('inc', 'fedora_repository', 'core/formClass');
       $metaDataForm = new formClass();
       $return_value = $metaDataForm->updateMetaData($form_state['values']['form_id'], $form_state['values'], $client);
       $form_state['storage'] = NULL;
@@ -819,7 +819,7 @@ function fedora_repository_edit_qdc_form_submit($form, &$form_state) {
  * creates a new permission than can be assigned to roles
  */
 function fedora_repository_perm() {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   return array(
     OBJECTHELPER::$OBJECT_HELPER_VIEW_FEDORA,
     OBJECTHELPER::$EDIT_FEDORA_METADATA,
@@ -844,7 +844,7 @@ function fedora_repository_perm() {
  * @return type 
  */
 function fedora_repository_access($op, $node, $account) {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   $objectHelper = new ObjectHelper();
   return $objectHelper->fedora_repository_access($op, $node, $account);
 }
@@ -879,7 +879,7 @@ function makeObject($pid, $dsID) {
     return ' ';
   }
 
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   $objectHelper = new ObjectHelper();
   $objectHelper->makeObject($pid, $dsID);
 }
@@ -898,7 +898,7 @@ function makeObject($pid, $dsID) {
  * @return type 
  */
 function fedora_repository_get_items($pid = NULL, $dsId = NULL, $collection = NULL, $page_number = NULL, $limit = NULL) {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   global $user;
@@ -958,9 +958,9 @@ function fedora_repository_get_items($pid = NULL, $dsId = NULL, $collection = NU
 
   $content = '<div id="content-fedora">';
 
-  module_load_include('inc', 'fedora_repository', 'CollectionClass');
+  module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
   $collectionClass = new CollectionClass();
-  module_load_include('inc', 'fedora_repository', 'ContentModel');
+  module_load_include('inc', 'fedora_repository', 'core/ContentModel');
   module_load_include('inc', 'fedora_repository', 'plugins/FedoraObjectDetailedContent');
   $breadcrumbs = array();
   $objectHelper->getBreadcrumbs($pid, $breadcrumbs);
@@ -1023,7 +1023,7 @@ function fedora_repository_urlencode_string($str) {
  */
 function fedora_object_as_attachment($pid, $dsId, $label=NULL, $version=NULL) {
   global $user;
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
 
   if ($pid == NULL || $dsId == NULL) {
     drupal_set_message(t("no pid or dsid given to create an object with!"));
@@ -1058,7 +1058,7 @@ function repository_page($pid = NULL, $dsId = NULL, $collection = NULL, $pageNum
  */
 function repository_service($pid = NULL, $servicePid = NULL, $serviceMethod = NULL) {
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   global $user;
 
   if (!fedora_repository_access(OBJECTHELPER::$OBJECT_HELPER_VIEW_FEDORA, $pid, $user)) {
@@ -1103,7 +1103,7 @@ function repository_service($pid = NULL, $servicePid = NULL, $serviceMethod = NU
  * @return array 
  */
 function fedora_repository_search($op = 'search', $keys = NULL) {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   module_load_include('inc', 'fedora_repository', 'api/fedora_utils');
 
   switch ($op) {
@@ -1444,7 +1444,7 @@ function fedora_repository_install_demos_page() {
  * @return string 
  */
 function fedora_repository_demo_objects_form() {
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   module_load_include('inc', 'fedora_repository', 'api/fedora_item');
   $form = array();
   $existing_demos = array();
@@ -1786,7 +1786,7 @@ function theme_fedora_repository_time($element) {
  */
 function fedora_repository_remove_item_from_basket($pid) {
 
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   $pids = empty($_SESSION['basket']['processed']) ? array() : $_SESSION['basket']['processed'];
 
   $objectHelper = new ObjectHelper();
@@ -1996,7 +1996,7 @@ function _fedora_repository_get_basket_pids() {
 
   $pids = empty($_SESSION['basket']['processed']) ? array() : $_SESSION['basket']['processed'];
 
-  module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+  module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   $ob = new ObjectHelper();
   foreach ($_SESSION['basket']['unprocessed'] as $pid) {
 // Check if the pid already exists in the tree
diff --git a/plugins/CollectionFormBuilder.inc b/plugins/CollectionFormBuilder.inc
index 83624d38..8cf698fd 100644
--- a/plugins/CollectionFormBuilder.inc
+++ b/plugins/CollectionFormBuilder.inc
@@ -30,7 +30,7 @@ class CollectionFormBuilder extends FormBuilder {
    * @param type $rootElement 
    */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     global $base_url;
 
     $mimetype = new MimeClass();
diff --git a/plugins/DarwinCore.inc b/plugins/DarwinCore.inc
index dc698521..129d91f3 100644
--- a/plugins/DarwinCore.inc
+++ b/plugins/DarwinCore.inc
@@ -243,8 +243,8 @@ class DarwinCore {
    */
   public function asHTML() {
     $path = drupal_get_path('module', 'Fedora_Repository');
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
-    module_load_include('inc', 'fedora_repository', 'CollectionClass');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
 
     $xmlstr = $this->darwinCoreXML;
     html_entity_decode($xmlstr);
diff --git a/plugins/DemoFormBuilder.inc b/plugins/DemoFormBuilder.inc
index 305c2029..e4fd4a9b 100644
--- a/plugins/DemoFormBuilder.inc
+++ b/plugins/DemoFormBuilder.inc
@@ -29,7 +29,7 @@ class DemoFormBuilder extends FormBuilder {
    * @param type $rootElement 
    */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     global $base_url;
     $mimetype = new MimeClass();
     $server = NULL;
diff --git a/plugins/DocumentConverter.inc b/plugins/DocumentConverter.inc
index ce782f08..3c231581 100644
--- a/plugins/DocumentConverter.inc
+++ b/plugins/DocumentConverter.inc
@@ -32,7 +32,7 @@ class DocumentConverter {
    * @return string 
    */
   function convert($parameterArray = NULL, $dsid, $file, $output_ext) {
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
 
     #debug:
     #drupal_set_message("Sending $file to ". $this->converter_service_url ." for convertsion to $output_ext", 'status');
diff --git a/plugins/Flv.inc b/plugins/Flv.inc
index 76506ce3..908d783e 100644
--- a/plugins/Flv.inc
+++ b/plugins/Flv.inc
@@ -137,7 +137,7 @@ class FormBuilder {
    * @param type $rootElement 
    */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     $mimetype = new MimeClass();
     $server = NULL;
     $file = $form_values['ingest-file-location'];
diff --git a/plugins/FlvFormBuilder.inc b/plugins/FlvFormBuilder.inc
index 5e022b88..7972909b 100644
--- a/plugins/FlvFormBuilder.inc
+++ b/plugins/FlvFormBuilder.inc
@@ -30,7 +30,7 @@ class FlvFormBuilder extends FormBuilder {
    */
 
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     global $base_url;
     $mimetype = new MimeClass();
     $server = NULL;
diff --git a/plugins/FormBuilder.inc b/plugins/FormBuilder.inc
index 02ca6ace..68a7eeaa 100644
--- a/plugins/FormBuilder.inc
+++ b/plugins/FormBuilder.inc
@@ -83,7 +83,7 @@ class FormBuilder {
    * @return type 
    */
   function createPolicy($collectionPid, &$dom, &$rootElement) {
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     $objectHelper = new ObjectHelper();
 
     $dsid = 'CHILD_SECURITY';
@@ -135,7 +135,7 @@ class FormBuilder {
    */
   function handleQDCForm($form_values) {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
-    module_load_include('inc', 'fedora_repository', 'CollectionPolicy');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionPolicy');
 
     $dom = new DomDocument("1.0", "UTF-8");
     $dom->formatOutput = TRUE;
@@ -195,7 +195,7 @@ class FormBuilder {
    * @param type $rootElement 
    */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement) {
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     global $base_url;
     $mimetype = new MimeClass();
     $server = NULL;
diff --git a/plugins/ImageManipulation.inc b/plugins/ImageManipulation.inc
index bbbe84fd..a67ad220 100644
--- a/plugins/ImageManipulation.inc
+++ b/plugins/ImageManipulation.inc
@@ -15,7 +15,7 @@ class ImageManipulation {
    * Constructor
    */
   function ImageManipulation() {
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
   }
 
   /**
diff --git a/plugins/ModsFormBuilder.inc b/plugins/ModsFormBuilder.inc
index c7eefdb6..2b62e209 100644
--- a/plugins/ModsFormBuilder.inc
+++ b/plugins/ModsFormBuilder.inc
@@ -24,7 +24,7 @@ class ModsFormBuilder extends FormBuilder {
   function __construct($pid=NULL) {
     parent::__construct();
     if ($pid !== NULL) {
-      module_load_include('inc', 'fedora_repository', 'ContentModel');
+      module_load_include('inc', 'fedora_repository', 'core/ContentModel');
       module_load_include('inc', 'fedora_repository', 'api/fedora_item');
 
       $this->pid = $pid;
@@ -256,7 +256,7 @@ class ModsFormBuilder extends FormBuilder {
    */
   function handleModsForm(&$form_values, &$form_state) {
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
-    module_load_include('inc', 'fedora_repository', 'CollectionPolicy');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionPolicy');
 
     $form_state['storage']['people'] = NULL; //clears out old entities for the next run of the formbuilder.
 
diff --git a/plugins/Refworks.inc b/plugins/Refworks.inc
index e539520c..50361526 100644
--- a/plugins/Refworks.inc
+++ b/plugins/Refworks.inc
@@ -223,8 +223,8 @@ class Refworks {
    */
   function handleForm(&$form_values) {
     $errorMessage = NULL;
-    module_load_include('inc', 'fedora_repository', 'CollectionClass');
-    module_load_include('inc', 'fedora_repository', 'ContentModel');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
+    module_load_include('inc', 'fedora_repository', 'core/ContentModel');
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     $contentModelPid = ContentModel::getPidFromIdentifier($form_values['models']);
     $contentModelDsid = ContentModel::getDSIDFromIdentifier($form_values['models']);
@@ -389,7 +389,7 @@ class Refworks {
    */
   function createFedoraDataStreams($form_values, &$dom, &$rootElement, $reference) {
     global $base_url;
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     $mimetype = new MimeClass();
     $server = NULL;
     $this->createRomeoDataStream($dom, $rootElement);
diff --git a/plugins/ShowStreamsInFieldSets.inc b/plugins/ShowStreamsInFieldSets.inc
index 3fc116d2..2e2328b2 100644
--- a/plugins/ShowStreamsInFieldSets.inc
+++ b/plugins/ShowStreamsInFieldSets.inc
@@ -143,7 +143,7 @@ class ShowStreamsInFieldSets {
    * @return type 
    */
   function showQdc() {
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     $objectHelper = new ObjectHelper();
     $content = $objectHelper->getQDC($this->pid);
     $collection_fieldset = array(
@@ -174,7 +174,7 @@ class ShowStreamsInFieldSets {
    */
   function showRefworks() {
     $path = drupal_get_path('module', 'fedora_repository');
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     $collectionHelper = new CollectionClass();
     $xmlstr = $collectionHelper->getStream($this->pid, "refworks");
     html_entity_decode($xmlstr);
@@ -227,7 +227,7 @@ class ShowStreamsInFieldSets {
    */
   function showRomeo($collapsed = FALSE) {
     $path = drupal_get_path('module', 'Fedora_Repository');
-    module_load_include('inc', 'fedora_repository', 'CollectionClass');
+    module_load_include('inc', 'fedora_repository', 'core/CollectionClass');
     $collectionHelper = new CollectionClass();
     $xmlstr = $collectionHelper->getStream($this->pid, "ROMEO", 0);
 
diff --git a/plugins/herbarium.inc b/plugins/herbarium.inc
index fa2ac4a7..1903da2c 100644
--- a/plugins/herbarium.inc
+++ b/plugins/herbarium.inc
@@ -75,7 +75,7 @@ class Herbarium {
      */
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     module_load_include('inc', 'fedora_repository', 'plugins/DarwinCore');
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     global $user;
     $mimetype = new MimeClass();
     $dwc = new DarwinCore($this->item);
@@ -97,7 +97,7 @@ class Herbarium {
      * Create fedora object
      * Add the datastreams
      */
-    module_load_include('inc', 'fedora_repository', 'MimeClass');
+    module_load_include('inc', 'fedora_repository', 'api/MimeClass');
     module_load_include('inc', 'fedora_repository', 'api/fedora_item');
     module_load_include('inc', 'fedora_repository', 'plugins/DarwinCore');
     global $user;
@@ -184,7 +184,7 @@ class Herbarium {
       '#title' => t('Darwin Core'),
       '#content' => $dwc->asHTML(),
     );
-    module_load_include('inc', 'fedora_repository', 'ObjectHelper');
+    module_load_include('inc', 'fedora_repository', 'api/ObjectHelper');
     $obj = new ObjectHelper();
     if (fedora_repository_access(OBJECTHELPER :: $EDIT_FEDORA_METADATA, $this->pid, $user)) {
       $editform = drupal_get_form('fedora_repository_edit_qdc_form', $this->pid, 'DARWIN_CORE');