Index: modules/simpletest/tests/file.test
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/tests/file.test,v
retrieving revision 1.7
diff -u -p -r1.7 file.test
--- modules/simpletest/tests/file.test	12 Oct 2008 06:37:40 -0000	1.7
+++ modules/simpletest/tests/file.test	5 Nov 2008 23:43:08 -0000
@@ -1018,14 +1018,14 @@ class FileValidateTest extends FileHookT
     // Use the file_test.module's test validator to ensure that passing tests
     // return correctly.
     file_test_reset();
-    $GLOBALS['file_test_hook_return']['validate'] = array();
+    file_test_set_return('validate', array());
     $passing = array('file_test_validator' => array(array()));
     $this->assertEqual(file_validate($file, $passing), array(), t('Validating passes.'));
     $this->assertFileHookCalled('validate', 1);
 
     // Now test for failures in validators passed in and by hook_validate.
     file_test_reset();
-    $GLOBALS['file_test_hook_return']['validate'] = array('Epic fail');
+    file_test_set_return('validate', array('Epic fail'));
     $failing = array('file_test_validator' => array(array('Failed', 'Badly')));
     $this->assertEqual(file_validate($file, $failing), array('Failed', 'Badly', 'Epic fail'), t('Validating returns errors.'));
     $this->assertFileHookCalled('validate', 1);
Index: modules/simpletest/tests/file_test.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/tests/file_test.module,v
retrieving revision 1.2
diff -u -p -r1.2 file_test.module
--- modules/simpletest/tests/file_test.module	9 Oct 2008 00:02:29 -0000	1.2
+++ modules/simpletest/tests/file_test.module	5 Nov 2008 23:43:08 -0000
@@ -54,10 +54,12 @@ function _file_test_form_submit(&$form, 
 
 /**
  * Reset/initialize the history of calls to the file_* hooks.
+ *
+ * @see the getter/setter functions file_test_get_calls() and file_test_reset().
  */
 function file_test_reset() {
   // Keep track of calls to these hooks
-  $GLOBALS['file_test_results'] = array(
+  $results = array(
     'load' => array(),
     'validate' => array(),
     'download' => array(),
@@ -69,30 +71,81 @@ function file_test_reset() {
     'move' => array(),
     'delete' => array(),
   );
+  variable_set('file_test_results', $results);
 
-  // These hooks will return these values.
-  $GLOBALS['file_test_hook_return'] = array(
-    'validate' => NULL,
+  // These hooks will return these values, @see file_test_set_return().
+  $return = array(
+    'validate' => array(),
     'download' => NULL,
     'references' => NULL,
   );
+  variable_set('file_test_return', $return);
 }
 
 /**
- * Get the values passed to a the hook calls for a given operation.
+ * Get the arguments passed to invocation of a given hook since
+ * file_test_reset() was last called.
  *
- * @param $op One of the hook_file_* operations.
- * @returns Array of the parameters passed to each call.
+ * @param $op
+ *   One of the hook_file_* operations: "load", "validate", etc.
+ * @returns
+ *   Array of the parameters passed to each call.
+ * @see _file_test_log_call() and file_test_reset()
  */
 function file_test_get_calls($op) {
-  return $GLOBALS['file_test_results'][$op];
+  $results = variable_get('file_test_results', array());
+  return $results[$op];
+}
+
+/**
+ * Store the values passed to a hook invocation.
+ *
+ * @param $op
+ *   One of the hook_file_* operations.
+ * @param $args
+ *   Values passed to hook.
+ * @see file_test_get_calls() and file_test_reset()
+ */
+function _file_test_log_call($op, $args) {
+  $results = variable_get('file_test_results', array());
+  $results[$op][] = $args;
+  variable_set('file_test_results', $results);
+}
+
+/**
+ * Load the appropriate return value.
+ *
+ * @param $op
+ *   One of the hook_file_[validate,download,references] operations.
+ * @return
+ *   Value set by file_test_set_return().
+* @see file_test_set_return() and file_test_reset().
+ */
+function _file_test_get_return($op) {
+  $return = variable_get('file_test_return', array($op => NULL));
+  return $return[$op];
+}
+
+/**
+ * Assign a return value for a given operation.
+ *
+ * @param $op
+ *   One of the hook_file_[validate,download,references] operations.
+ * @param $value
+ *   Value for the hook to return.
+ * @see _file_test_get_return() and file_test_reset().
+ */
+function file_test_set_return($op, $value) {
+  $return = variable_get('file_test_return', array());
+  $return[$op] = $value;
+  variable_set('file_test_return', $return);
 }
 
 /**
  * Implementation of hook_file_load().
  */
-function file_test_file_load(&$file) {
-  $GLOBALS['file_test_results']['load'][] = func_get_args();
+function file_test_file_load($file) {
+  _file_test_log_call('load', array($file));
   // Assign a value on the object so that we can test that the $file is passed
   // by reference.
   $file->file_test['loaded'] = TRUE;
@@ -101,66 +154,65 @@ function file_test_file_load(&$file) {
 /**
  * Implementation of hook_file_validate().
  */
-function file_test_file_validate(&$file) {
-  $GLOBALS['file_test_results']['validate'][] = func_get_args();
-  return $GLOBALS['file_test_hook_return']['validate'];
+function file_test_file_validate($file) {
+  _file_test_log_call('validate', array($file));
+  return _file_test_get_return('validate');
 }
 
 /**
  * Implementation of hook_file_status().
  */
-function file_test_file_status(&$file) {
-  $GLOBALS['file_test_results']['status'][] = func_get_args();
+function file_test_file_status($file) {
+  _file_test_log_call('status', array($file));
 }
 
 /**
  * Implementation of hook_file_download().
  */
-function file_test_file_download(&$file) {
-  $GLOBALS['file_test_results']['download'][] = func_get_args();
-  return $GLOBALS['file_test_hook_return']['download'];
+function file_test_file_download($file) {
+  _file_test_log_call('download', array($file));
+  return _file_test_get_return('download');
 }
 
 /**
  * Implementation of hook_file_references().
  */
-function file_test_file_references(&$file) {
-  $GLOBALS['file_test_results']['references'][] = func_get_args();
-  return $GLOBALS['file_test_hook_return']['references'];
+function file_test_file_references($file) {
+  _file_test_log_call('references', array($file));
+  return _file_test_get_return('references');
 }
 
 /**
  * Implementation of hook_file_insert().
  */
-function file_test_file_insert(&$file) {
-  $GLOBALS['file_test_results']['insert'][] = func_get_args();
+function file_test_file_insert($file) {
+  _file_test_log_call('insert', array($file));
 }
 
 /**
  * Implementation of hook_file_update().
  */
-function file_test_file_update(&$file) {
-  $GLOBALS['file_test_results']['update'][] = func_get_args();
+function file_test_file_update($file) {
+  _file_test_log_call('update', array($file));
 }
 
 /**
  * Implemenation of hook_file_copy().
  */
-function file_test_file_copy(&$file, &$source) {
-  $GLOBALS['file_test_results']['copy'][] = func_get_args();
+function file_test_file_copy($file, $source) {
+  _file_test_log_call('copy', array($file, $source));
 }
 
 /**
  * Implemenation of hook_file_move().
  */
-function file_test_file_move(&$file, &$source) {
-  $GLOBALS['file_test_results']['move'][] = func_get_args();
+function file_test_file_move($file, $source) {
+  _file_test_log_call('move', array($file, $source));
 }
 
 /**
  * Implementation of hook_file_delete().
  */
-function file_test_file_delete(&$file) {
-  $GLOBALS['file_test_results']['delete'][] = func_get_args();
+function file_test_file_delete($file) {
+  _file_test_log_call('delete', array($file));
 }
-
Index: modules/system/system.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.module,v
retrieving revision 1.635
diff -u -p -r1.635 system.module
--- modules/system/system.module	31 Oct 2008 02:18:22 -0000	1.635
+++ modules/system/system.module	5 Nov 2008 23:43:08 -0000
@@ -1426,18 +1426,15 @@ function system_cron() {
   db_query('DELETE FROM {batch} WHERE timestamp < %d', REQUEST_TIME - 864000);
 
   // Remove temporary files that are older than DRUPAL_MAXIMUM_TEMP_FILE_AGE.
-  $result = db_query('SELECT * FROM {files} WHERE status = %d and timestamp < %d', FILE_STATUS_TEMPORARY, REQUEST_TIME - DRUPAL_MAXIMUM_TEMP_FILE_AGE);
-  while ($file = db_fetch_object($result)) {
-    if (file_exists($file->filepath)) {
-      // If files that exist cannot be deleted, continue so the database remains
-      // consistent.
+  $result = db_query('SELECT fid FROM {files} WHERE status & :permanent != :permanent AND timestamp < :timestamp', array(':permanent' => FILE_STATUS_PERMANENT, ':timestamp' => REQUEST_TIME - DRUPAL_MAXIMUM_TEMP_FILE_AGE));
+  foreach ($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);
-        continue;
       }
     }
-    db_query('DELETE FROM {files} WHERE fid = %d', $file->fid);
   }
+
   $core = array('cache', 'cache_block', 'cache_filter', 'cache_page', 'cache_form', 'cache_menu');
   $cache_tables = array_merge(module_invoke_all('flush_caches'), $core);
   foreach ($cache_tables as $table) {
Index: modules/system/system.test
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.test,v
retrieving revision 1.23
diff -u -p -r1.23 system.test
--- modules/system/system.test	1 Nov 2008 21:21:35 -0000	1.23
+++ modules/system/system.test	5 Nov 2008 23:43:08 -0000
@@ -252,6 +252,41 @@ class CronRunTestCase extends DrupalWebT
     // Execute cron directly.
     $this->assertTrue(drupal_cron_run(), t('Cron ran successfully.'));
   }
+
+  /**
+   * Ensure that temporary files are removed.
+   */
+  function testTempFileCleanup() {
+    // Create files for all the possible combinations of age and status. We're
+    // using UPDATE statments rather than file_save() because it would set the
+    // timestamp.
+
+    // Temporary file that's older than DRUPAL_MAXIMUM_TEMP_FILE_AGE.
+    $temp_old = file_save_data('');
+    db_query('UPDATE {files} SET status = :status, timestamp = :timestamp WHERE fid = :fid', array(':status' => FILE_STATUS_TEMPORARY, ':timestamp' => 1, ':fid' => $temp_old->fid));
+    $this->assertTrue(file_exists($temp_old->filepath), t('Old temp file was created correctly.'));
+
+    // Temporary file that's less than DRUPAL_MAXIMUM_TEMP_FILE_AGE.
+    $temp_new = file_save_data('');
+    db_query('UPDATE {files} SET status = :status WHERE fid = :fid', array(':status' => FILE_STATUS_TEMPORARY, ':fid' => $temp_new->fid));
+    $this->assertTrue(file_exists($temp_new->filepath), t('New temp file was created correctly.'));
+
+    // Permanent file that's older than DRUPAL_MAXIMUM_TEMP_FILE_AGE.
+    $perm_old = file_save_data('');
+    db_query('UPDATE {files} SET timestamp = :timestamp WHERE fid = :fid', array(':timestamp' => 1, ':fid' => $perm_old->fid));
+    $this->assertTrue(file_exists($perm_old->filepath), t('Old permanent file was created correctly.'));
+
+    // Permanent file that's newer than DRUPAL_MAXIMUM_TEMP_FILE_AGE.
+    $perm_new = file_save_data('');
+    $this->assertTrue(file_exists($perm_new->filepath), t('New permanent file was created correctly.'));
+
+    // Run cron and then ensure that only the old, temp file was deleted.
+    $this->assertTrue(drupal_cron_run(), t('Cron ran successfully.'));
+    $this->assertFalse(file_exists($temp_old->filepath), t('Old temp file was correctly removed.'));
+    $this->assertTrue(file_exists($temp_new->filepath), t('New temp file was correctly ignored.'));
+    $this->assertTrue(file_exists($perm_old->filepath), t('Old permanent file was correctly ignored.'));
+    $this->assertTrue(file_exists($perm_new->filepath), t('New permanent file was correctly ignored.'));
+  }
 }
 
 class AdminOverviewTestCase extends DrupalWebTestCase {