diff --git includes/file.inc includes/file.inc
index 6a28a0c..908693c 100644
--- includes/file.inc
+++ includes/file.inc
@@ -348,6 +348,103 @@ function file_save($file) {
 }
 
 /**
+ * Determine where a file is used.
+ *
+ * @param $file
+ *   A file object.
+ * @return
+ *   An nested array with usage data. The first level is keyed by module
+ *   name, the second by table name, the third has 'id' and 'count' keys.
+ *
+ * @see file_add_usage()
+ * @see file_remove_usage()
+ */
+function file_get_usage(stdClass $file) {
+  $result = db_query('SELECT f.module, f.type, f.id, f.count FROM {file_usage} f WHERE f.fid = :fid AND count > 0', array(':fid' => $file->fid));
+  $references = array();
+
+  foreach ($result as $usage) {
+    $references[$usage->module][$usage->type] = array('id' => $usage->id, 'count' => $usage->count);
+  }
+  return $references;
+}
+
+/**
+ * Inform Drupal that a module is using a file.
+ *
+ * This usage information will be queried during file_delete().
+ *
+ * Examples:
+ * - The upload module that associates files with node revisions so the
+ *   @p $type would be 'node_revision' and @p $id would be the node's vid.
+ * - The user module associates an image with a user so the @p $type would be
+ *   'user' and the $id would be the user's id.
+ *
+ * @param $file
+ *   A file object.
+ * @param $module
+ *   The name of the module using the file.
+ * @param $type
+ *   The name of the table where the file is referenced.
+ * @param $id
+ *   The id of the row in the table.
+ *
+ * @see file_get_usage()
+ * @see file_remove_usage()
+ */
+function file_add_usage(stdClass $file, $module, $type, $id) {
+  db_merge('file_usage')
+    ->key(array(
+      'fid' => $file->fid,
+      'module' => $module,
+      'type' => $type,
+      'id' => $id,
+    ))
+    ->fields(array('count' => 1))
+    ->expression('count', 'count + 1')
+    ->execute();
+}
+
+/**
+ * Inform Drupal that a module is no longer using a file.
+ *
+ * If no usages of the file remain in the database, the file itself will be
+ * deleted using file_delete().
+ *
+ * @param $file
+ *   A file object.
+ * @param $module
+ *   The name of the module using the file.
+ * @param $type
+ *   The name of the table where the file is referenced.
+ * @param $id
+ *   The id of the row in the table.
+ * @return
+ *   TRUE for success, or FALSE if no usages remain but the file still could
+ *   not be deleted.
+ *
+ * @see file_add_usage()
+ * @see file_get_usage()
+ * @see file_delete()
+ */
+function file_remove_usage(stdClass $file, $module, $type, $id) {
+  db_update('file_usage')->expression('count', 'count - 1')
+    ->condition('fid', $file->fid)
+    ->condition('module', $module)
+    ->condition('type', $type)
+    ->condition('id', $id)
+    ->execute();
+
+  // Delete the file, unless it is still in use somewhere.
+  $references = db_result(db_query('SELECT COUNT(*) FROM {file_usage} f WHERE f.fid = :fid AND count > 0', array(':fid' => $file->fid)));
+  $args = func_get_args();
+  if (empty($references)) {
+    return file_delete($file);
+  }
+  return TRUE;
+}
+
+/**
  * Copy a file to a new location and adds a file record to the database.
  *
  * This function should be used when manipulating files that have records
@@ -724,34 +821,19 @@ function file_create_filename($basename, $directory) {
 /**
  * Delete a file and its database record.
  *
- * If the $force parameter is not TRUE hook_file_references() will be called
- * to determine if the file is being used by any modules. If the file is being
- * used is the delete will be canceled.
- *
  * @param $file
  *   A file object.
- * @param $force
- *   Boolean indicating that the file should be deleted even if
- *   hook_file_references() reports that the file is in use.
- * @return mixed
- *   TRUE for success, FALSE in the event of an error, or an array if the file
- *   is being used by another module. The array keys are the module's name and
- *   the values are the number of references.
+ * @return
+ *   TRUE for success, or FALSE in the event of an error.
  *
  * @see file_unmanaged_delete()
- * @see hook_file_references()
+ * @see file_get_usage()
+ * @see file_remove_usage()
  * @see hook_file_delete()
  */
-function file_delete($file, $force = FALSE) {
+function file_delete($file) {
   $file = (object)$file;
 
-  // If any module returns a value from the reference hook, the file will not
-  // be deleted from Drupal, but file_delete will return a populated array that
-  // tests as TRUE.
-  if (!$force && ($references = module_invoke_all('file_references', $file))) {
-    return $references;
-  }
-
   // Let other modules clean up any references to the deleted file.
   module_invoke_all('file_delete', $file);
 
@@ -759,6 +841,7 @@ function file_delete($file, $force = FALSE) {
   // database, so UIs can still find the file in the database.
   if (file_unmanaged_delete($file->filepath)) {
     db_delete('files')->condition('fid', $file->fid)->execute();
+    db_delete('file_usage')->condition('fid', $file->fid)->execute();
     return TRUE;
   }
   return FALSE;
diff --git modules/node/node.api.php modules/node/node.api.php
index 3be7752..4c647cb 100644
--- modules/node/node.api.php
+++ modules/node/node.api.php
@@ -291,7 +291,7 @@ function hook_node_delete_revision($node) {
     return;
   }
   foreach ($node->files as $file) {
-    file_delete($file);
+    file_remove_usage($file);
   }
 }
 
diff --git modules/simpletest/tests/file.test modules/simpletest/tests/file.test
index 18bc651..9f0ae75 100644
--- modules/simpletest/tests/file.test
+++ modules/simpletest/tests/file.test
@@ -223,13 +223,13 @@ class FileHookTestCase extends FileTestCase {
       $this->assertTrue(FALSE, t('Expected hooks %expected to be called but %uncalled was not called.', array('%expected' => implode(', ', $expected), '%uncalled' => implode(', ', $uncalled))));
     }
     else {
-      $this->assertTrue(TRUE, t('All the expected hooks were called: %expected', array('%expected' => implode(', ', $expected))));
+      $this->assertTrue(TRUE, t('All the expected hooks were called: %expected', array('%expected' => empty($expected) ? t('(none)') : implode(', ', $expected))));
     }
 
     // Determine if there were any unexpected calls.
     $unexpected = array_diff($actual, $expected);
     if (count($unexpected)) {
-      $this->assertTrue(FALSE, t('Unexpected hooks were called: %unexpected.', array('%unexpected' => implode(', ', $unexpected))));
+      $this->assertTrue(FALSE, t('Unexpected hooks were called: %unexpected.', array('%unexpected' => empty($unexpected) ? t('(none)') : implode(', ', $unexpected))));
     }
     else {
       $this->assertTrue(TRUE, t('No unexpected hooks were called.'));
@@ -1245,18 +1245,42 @@ class FileDeleteTest extends FileHookTestCase {
   /**
    * Try deleting a normal file (as opposed to a directory, symlink, etc).
    */
-  function testNormal() {
+  function testUnused() {
     $file = $this->createFile();
 
     // Check that deletion removes the file and database record.
-    $this->assertTrue(is_file($file->filepath), t("File exists."));
-    $this->assertIdentical(file_delete($file), TRUE, t("Delete worked."));
-    $this->assertFileHooksCalled(array('references', 'delete'));
-    $this->assertFalse(file_exists($file->filepath), t("Test file has actually been deleted."));
+    $this->assertTrue(is_file($file->filepath), t('File exists.'));
+    $this->assertIdentical(file_delete($file), TRUE, t('Delete worked.'));
+    $this->assertFileHooksCalled(array('delete'));
+    $this->assertFalse(file_exists($file->filepath), t('Test file has actually been deleted.'));
     $this->assertFalse(file_load($file->fid), t('File was removed from the database.'));
+    $this->assertFalse(file_get_usage($file), t('File usage data was removed.'));
+  }
+
+  /**
+   * Try deleting a file that is in use.
+   */
+  function testInUse() {
+    $file = $this->createFile();
+    file_add_usage($file, 'testing', 'test', 1);
+    file_add_usage($file, 'testing', 'test', 1);
+
+    file_remove_usage($file, 'testing', 'test', 1);
+    $usage = file_get_usage($file);
+    $this->assertFileHooksCalled(array());
+    $this->assertEqual($usage['testing']['test'], array('id' => 1, 'count' => 1), t('Test file is still in use.'));
+    $this->assertTrue(file_exists($file->filepath), t('File still exists on the disk.'));
+    $this->assertTrue(file_load($file->fid), t('File still exists in the database.'));
+
+    // Clear out the call to hook_file_load().
+    file_test_reset();
 
-    // TODO: implement hook_file_references() in file_test.module and report a
-    // file in use and test the $force parameter.
+    file_remove_usage($file, 'testing', 'test', 1);
+    $usage = file_get_usage($file);
+    $this->assertFileHooksCalled(array('delete'));
+    $this->assertTrue(empty($usage), t('File usage data was removed.'));
+    $this->assertFalse(file_exists($file->filepath), t('File has been deleted after its last usage was removed.'));
+    $this->assertFalse(file_load($file->fid), t('File was removed from the database.'));
   }
 }
 
@@ -1358,7 +1382,7 @@ class FileMoveTest extends FileHookTestCase {
     $this->assertTrue($result, t('File moved sucessfully.'));
 
     // Check that the correct hooks were called.
-    $this->assertFileHooksCalled(array('move', 'update', 'delete', 'references', 'load'));
+    $this->assertFileHooksCalled(array('move', 'update', 'delete', 'load'));
 
     // Reload the file from the database and check that the changes were
     // actually saved.
@@ -1720,6 +1744,91 @@ class FileSaveTest extends FileHookTestCase {
   }
 }
 
+/**
+ * Tests the file_get_usage(), file_add_usage() and file_remove_usage()
+ * functions.
+ */
+class FileUsageTest extends FileTestCase {
+  function getInfo() {
+    return array(
+      'name' => t('File usage'),
+      'description' => t('Tests the file usage functions.'),
+      'group' => t('File'),
+    );
+  }
+
+  /**
+   * Test the file_get_usage() function.
+   */
+  function testGetUsage() {
+    $file = $this->createFile();
+    db_insert('file_usage')->fields(array(
+      'fid' => $file->fid,
+      'module' => 'testing',
+      'type' => 'foo',
+      'id' => 1,
+      'count' => 1
+    ))->execute();
+    db_insert('file_usage')->fields(array(
+      'fid' => $file->fid,
+      'module' => 'testing',
+      'type' => 'bar',
+      'id' => 2,
+      'count' => 2
+    ))->execute();
+
+    $usage = file_get_usage($file);
+
+    $this->assertEqual(count($usage['testing']), 2, t('Returned the correct number of items.'));
+    $this->assertEqual($usage['testing']['foo']['id'], 1, t('Returned the correct id.'));
+    $this->assertEqual($usage['testing']['bar']['id'], 2, t('Returned the correct id.'));
+    $this->assertEqual($usage['testing']['foo']['count'], 1, t('Returned the correct count.'));
+    $this->assertEqual($usage['testing']['bar']['count'], 2, t('Returned the correct count.'));
+  }
+
+  /**
+   * Test the file_add_usage() function.
+   */
+  function testAddUsage() {
+    $file = $this->createFile();
+    file_add_usage($file, 'testing', 'foo', 1);
+    // Add the file twice to ensure that the count is incremented rather than
+    // creating additional records.
+    file_add_usage($file, 'testing', 'bar', 2);
+    file_add_usage($file, 'testing', 'bar', 2);
+
+    $usage = db_select('file_usage', 'f')->fields('f')->condition('f.fid', $file->fid)->execute()->fetchAllAssoc('id');
+    $this->assertEqual(count($usage), 2, t('Created two records'));
+    $this->assertEqual($usage[1]->module, 'testing', t('Correct module'));
+    $this->assertEqual($usage[2]->module, 'testing', t('Correct module'));
+    $this->assertEqual($usage[1]->type, 'foo', t('Correct type'));
+    $this->assertEqual($usage[2]->type, 'bar', t('Correct type'));
+    $this->assertEqual($usage[1]->count, 1, t('Correct count'));
+    $this->assertEqual($usage[2]->count, 2, t('Correct count'));
+  }
+
+  /**
+   * Test the file_remove_usage() function.
+   */
+  function testRemoveUsage() {
+    $file = $this->createFile();
+    db_insert('file_usage')->fields(array(
+      'fid' => $file->fid,
+      'module' => 'testing',
+      'type' => 'bar',
+      'id' => 2,
+      'count' => 2
+    ))->execute();
+
+    file_remove_usage($file, 'testing', 'bar', 2);
+    $count = db_select('file_usage', 'f')->fields('f', array('count'))->condition('f.fid', $file->fid)->execute()->fetchField();
+    $this->assertEqual(1, $count, t('The count was decremented correctly.'));
+
+    file_remove_usage($file, 'testing', 'bar', 2);
+    $count = db_select('file_usage', 'f')->fields('f', array('count'))->condition('f.fid', $file->fid)->execute()->fetchField();
+    $this->assertEqual(0, $count, t('The count was decremented correctly.'));
+  }
+}
 
 /**
  * Tests the file_validate() function..
diff --git modules/simpletest/tests/file_test.module modules/simpletest/tests/file_test.module
index 06aa4ad..ba0a09c 100644
--- modules/simpletest/tests/file_test.module
+++ modules/simpletest/tests/file_test.module
@@ -77,7 +77,6 @@ function file_test_reset() {
     'load' => array(),
     'validate' => array(),
     'download' => array(),
-    'references' => array(),
     'insert' => array(),
     'update' => array(),
     'copy' => array(),
@@ -90,7 +89,6 @@ function file_test_reset() {
   $return = array(
     'validate' => array(),
     'download' => NULL,
-    'references' => NULL,
   );
   variable_set('file_test_return', $return);
 }
@@ -101,7 +99,7 @@ function file_test_reset() {
  *
  * @param $op
  *   One of the hook_file_* operations: 'load', 'validate', 'download',
- *   'references', 'insert', 'update', 'copy', 'move', 'delete'.
+ *   'insert', 'update', 'copy', 'move', 'delete'.
  * @returns
  *   Array of the parameters passed to each call.
  * @see _file_test_log_call() and file_test_reset()
@@ -115,9 +113,9 @@ function file_test_get_calls($op) {
  * Get an array with the calls for all hooks.
  *
  * @return
- *   An array keyed by hook name ('load', 'validate', 'download',
- *   'references', 'insert', 'update', 'copy', 'move', 'delete') with values
- *   being arrays of parameters passed to each call.
+ *   An array keyed by hook name ('load', 'validate', 'download', 'insert',
+ *   'update', 'copy', 'move', 'delete') with values being arrays of parameters
+ *   passed to each call.
  */
 function file_test_get_all_calls() {
   return variable_get('file_test_results', array());
@@ -128,7 +126,7 @@ function file_test_get_all_calls() {
  *
  * @param $op
  *   One of the hook_file_* operations: 'load', 'validate', 'download',
- *   'references', 'insert', 'update', 'copy', 'move', 'delete'.
+ *   'insert', 'update', 'copy', 'move', 'delete'.
  * @param $args
  *   Values passed to hook.
  * @see file_test_get_calls() and file_test_reset()
@@ -143,7 +141,7 @@ function _file_test_log_call($op, $args) {
  * Load the appropriate return value.
  *
  * @param $op
- *   One of the hook_file_[validate,download,references] operations.
+ *   One of the hook_file_[validate,download] operations.
  * @return
  *   Value set by file_test_set_return().
 * @see file_test_set_return() and file_test_reset().
@@ -157,7 +155,7 @@ function _file_test_get_return($op) {
  * Assign a return value for a given operation.
  *
  * @param $op
- *   One of the hook_file_[validate,download,references] operations.
+ *   One of the hook_file_[validate,download] operations.
  * @param $value
  *   Value for the hook to return.
  * @see _file_test_get_return() and file_test_reset().
@@ -197,14 +195,6 @@ function file_test_file_download($file) {
 }
 
 /**
- * Implement hook_file_references().
- */
-function file_test_file_references($file) {
-  _file_test_log_call('references', array($file));
-  return _file_test_get_return('references');
-}
-
-/**
  * Implement hook_file_insert().
  */
 function file_test_file_insert($file) {
diff --git modules/system/system.api.php modules/system/system.api.php
index 3f4f2c5..5dfc781 100644
--- modules/system/system.api.php
+++ modules/system/system.api.php
@@ -1179,6 +1179,13 @@ function hook_file_copy($file, $source) {
 /**
  * Respond to a file that has been moved.
  *
+ * $file->fid stays the same except if the moved file replaced a previously
+ * existing one, in which case the fid and filename of the existing target file
+ * is adopted for the new file object.
+ *
+ * Implement this hook if your module keeps track of files in a module-specific
+ * table, so that file references remain valid.
+ *
  * @param $file
  *   The updated file object after the move.
  * @param $source
@@ -1189,31 +1196,11 @@ function hook_file_copy($file, $source) {
  * @see file_move()
  */
 function hook_file_move($file, $source) {
-
-}
-
-/**
- * Report the number of times a file is referenced by a module.
- *
- * This hook is called to determine if a files is in use. Multiple modules may
- * be referencing the same file and to prevent one from deleting a file used by
- * another this hook is called.
- *
- * @param $file
- *   The file object being checked for references.
- * @return
- *   If the module uses this file return an array with the module name as the
- *   key and the value the number of times the file is used.
- *
- * @see file_delete()
- * @see upload_file_references()
- */
-function hook_file_references($file) {
-  // If upload.module is still using a file, do not let other modules delete it.
-  $file_used = (bool) db_query_range('SELECT 1 FROM {upload} WHERE fid = :fid', array(':fid' => $file->fid), 0, 1)->fetchField();
-  if ($file_used) {
-    // Return the name of the module and how many references it has to the file.
-    return array('upload' => $count);
+  if ($file->fid != $source->fid) {
+    db_update('upload')
+      ->fields(array('fid' => $file->fid))
+      ->condition('fid', $source->fid, '=')
+      ->execute();
   }
 }
 
diff --git modules/system/system.install modules/system/system.install
index 8230b78..190296e 100644
--- modules/system/system.install
+++ modules/system/system.install
@@ -686,6 +686,50 @@ function system_schema() {
     ),
   );
 
+  $schema['file_usage'] = array(
+    'description' => 'Track where a file is used.',
+    'fields' => array(
+      'fid' => array(
+        'description' => 'File ID.',
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+      ),
+      'module' => array(
+        'description' => 'The name of the module that is using the file.',
+        'type' => 'varchar',
+        'length' => 255,
+        'not null' => TRUE,
+        'default' => '',
+      ),
+      'type' => array(
+        'description' => 'The name of the table where the file is used.',
+        'type' => 'varchar',
+        'length' => 64,
+        'not null' => TRUE,
+        'default' => '',
+      ),
+      'id' => array(
+        'description' => 'The primary key of the object using the file.',
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+        'default' => 0,
+      ),
+      'count' => array(
+        'description' => 'The number of times this file is used by this object.',
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+        'default' => 0,
+      ),
+    ),
+    'primary key' => array('fid', 'type', 'id', 'module'),
+    'indexes' => array(
+      'type_id' => array('type', 'id'),
+    ),
+  );
+
   $schema['flood'] = array(
     'description' => 'Flood controls the threshold of events, such as the number of contact attempts.',
     'fields' => array(
@@ -2131,6 +2175,59 @@ function system_update_7028() {
 
 
 /**
+ * Create the file_usage table.
+ */
+function system_update_7029() {
+  $schema['file_usage'] = array(
+    'description' => 'Track where a file is used.',
+    'fields' => array(
+      'fid' => array(
+        'description' => 'File ID.',
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+      ),
+      'module' => array(
+        'description' => 'The name of the module that is using the file.',
+        'type' => 'varchar',
+        'length' => 255,
+        'not null' => TRUE,
+        'default' => '',
+      ),
+      'type' => array(
+        'description' => 'The name of the table where the file is used.',
+        'type' => 'varchar',
+        'length' => 64,
+        'not null' => TRUE,
+        'default' => '',
+      ),
+      'id' => array(
+        'description' => 'The primary key of the object using the file.',
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+        'default' => 0,
+      ),
+      'count' => array(
+        'description' => 'The number of times this file is used by this object.',
+        'type' => 'int',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+        'default' => 0,
+      ),
+    ),
+    'primary key' => array('fid', 'type', 'id', 'module'),
+    'indexes' => array(
+      'type_id' => array('type', 'id'),
+    ),
+  );
+
+  $ret = array();
+  db_create_table($ret, 'file_usage', $schema['file_usage']);
+  return $ret;
+}
+
+/**
  * @} End of "defgroup updates-6.x-to-7.x"
  * The next series of updates should start at 8000.
  */
diff --git modules/system/system.module modules/system/system.module
index 0f31158..42dd78c 100644
--- modules/system/system.module
+++ modules/system/system.module
@@ -1755,8 +1755,12 @@ function system_cron() {
   ));
   foreach ($result as $row) {
     if ($file = file_load($row->fid)) {
-      if (!file_delete($file)) {
-        watchdog('file system', 'Could not delete temporary file "%path" during garbage collection', array('%path' => $file->filepath), WATCHDOG_ERROR);
+      $references = file_get_usage($file);
+      if (empty($references)) {
+        file_delete($file);
+      }
+      else {
+        watchdog('file system', 'Could not delete temporary file "%path" during garbage collection, usage references left.', array('%path' => $file->filepath), WATCHDOG_ERROR);
       }
     }
   }
diff --git modules/upload/upload.install modules/upload/upload.install
index 0fa9d05..e5a5c89 100644
--- modules/upload/upload.install
+++ modules/upload/upload.install
@@ -97,4 +97,11 @@ function upload_schema() {
   return $schema;
 }
 
-
+/**
+ * Create file_usage records for our files.
+ */
+function upload_update_7000() {
+  $ret = array();
+  $ret[] = update_sql("INSERT INTO {file_usage} (fid, module, type, id, count) SELECT fid, 'upload', 'node_revision', vid, 1 FROM {upload}");
+  return $ret;
+}
diff --git modules/upload/upload.module modules/upload/upload.module
index 56ab028..904cbe0 100644
--- modules/upload/upload.module
+++ modules/upload/upload.module
@@ -277,14 +277,14 @@ function upload_file_load($files) {
 }
 
 /**
- * Implement hook_file_references().
+ * Implement hook_file_move().
  */
-function upload_file_references($file) {
-  // If upload.module is still using a file, do not let other modules delete it.
-  $file_used = (bool) db_query_range('SELECT 1 FROM {upload} WHERE fid = :fid', array(':fid' => $file->fid), 0, 1)->fetchField();
-  if ($file_used) {
-    // Return the name of the module and how many references it has to the file.
-    return array('upload' => $count);
+function upload_file_move($file, $source) {
+  if ($file->fid != $source->fid) {
+    db_update('upload')
+      ->fields(array('fid' => $file->fid))
+      ->condition('fid', $source->fid, '=')
+      ->execute();
   }
 }
 
@@ -407,7 +407,7 @@ function upload_node_delete($node) {
     return;
   }
   foreach ($node->files as $file) {
-    file_delete($file);
+    file_remove_usage($file);
   }
 }
 
@@ -420,7 +420,7 @@ function upload_node_delete_revision($node) {
     return;
   }
   foreach ($node->files as $file) {
-    file_delete($file);
+    file_remove_usage($file);
   }
 }
 
@@ -488,8 +488,7 @@ function upload_save($node) {
     if (!empty($file->remove)) {
       // Remove the reference from this revision.
       db_delete('upload')->condition('fid', $file->fid)->condition('vid', $node->vid)->execute();
-      // Try a soft delete, if the file isn't used elsewhere it'll be deleted.
-      file_delete($file);
+      $blah = file_remove_usage($file, 'upload', 'node_revision', $node->vid);
       // Remove it from the session in the case of new uploads,
       // that you want to disassociate before node submission.
       unset($node->files[$fid]);
@@ -497,6 +496,8 @@ function upload_save($node) {
       continue;
     }
 
+    $add_usage = FALSE;
+
     // Create a new revision, or associate a new file needed.
     if (!empty($node->old_vid) || $file->new) {
       db_insert('upload')
@@ -509,6 +510,7 @@ function upload_save($node) {
           'weight' => $file->weight,
         ))
         ->execute();
+      $add_usage = TRUE;
     }
     // Update existing revision.
     else {
@@ -524,6 +526,10 @@ function upload_save($node) {
     }
     $file->status |= FILE_STATUS_PERMANENT;
     $file = file_save($file);
+
+    if ($add_usage) {
+      file_add_usage($file, 'upload', 'node_revision', $node->vid);
+    }
   }
 }
 
diff --git modules/user/user.module modules/user/user.module
index bf360d6..09ca5b5 100644
--- modules/user/user.module
+++ modules/user/user.module
@@ -435,9 +435,14 @@ function user_save($account, $edit = array(), $category = 'account') {
         if ($picture = file_move($picture, $destination, FILE_EXISTS_REPLACE)) {
           $picture->status |= FILE_STATUS_PERMANENT;
           $edit['picture'] = file_save($picture);
+          file_add_usage($picture, 'user', 'user', $account->uid);
         }
       }
     }
+    // If the picture existed before and was unset, remove our reference to it.
+    elseif (!empty($account->picture->fid)) {
+      file_remove_usage($account->picture, 'user', 'user', $account->uid);
+    }
     $edit['picture'] = empty($edit['picture']->fid) ? 0 : $edit['picture']->fid;
 
     $edit['data'] = $data;
@@ -455,13 +460,6 @@ function user_save($account, $edit = array(), $category = 'account') {
       // return FALSE;
     }
 
-    // If the picture changed or was unset, remove the old one. This step needs
-    // to occur after updating the {users} record so that user_file_references()
-    // doesn't report it in use and block the deletion.
-    if (!empty($account->picture->fid) && ($edit['picture'] != $account->picture->fid)) {
-      file_delete($account->picture);
-    }
-
     // Reload user roles if provided.
     if (isset($edit['roles']) && is_array($edit['roles'])) {
       db_delete('users_roles')
@@ -828,14 +826,14 @@ function user_file_download($filepath) {
 }
 
 /**
- * Implement hook_file_references().
+ * Implement hook_file_move().
  */
-function user_file_references($file) {
-  // Determine if the file is used by this module.
-  $file_used = (bool) db_query_range('SELECT 1 FROM {users} WHERE picture = :fid', array(':fid' => $file->fid), 0, 1)->fetchField();
-  if ($file_used) {
-    // Return the name of the module and how many references it has to the file.
-    return array('user' => $count);
+function user_file_move($file, $source) {
+  if ($file->fid != $source->fid) {
+    db_update('users')
+      ->fields(array('picture' => $file->fid))
+      ->condition('picture', $source->fid, '=')
+      ->execute();
   }
 }