Index: install.php
===================================================================
RCS file: /cvs/drupal/drupal/install.php,v
retrieving revision 1.156
diff -u -9 -p -r1.156 install.php
--- install.php	18 Feb 2009 15:07:26 -0000	1.156
+++ install.php	22 Feb 2009 13:02:25 -0000
@@ -414,19 +414,19 @@ function install_find_profiles() {
  *   The selected profile.
  */
 function install_select_profile() {
   include_once DRUPAL_ROOT . '/includes/form.inc';
 
   $profiles = install_find_profiles();
   // Don't need to choose profile if only one available.
   if (sizeof($profiles) == 1) {
     $profile = array_pop($profiles);
-    require_once $profile->filename;
+    require_once $profile->filepath;
     return $profile->name;
   }
   elseif (sizeof($profiles) > 1) {
     foreach ($profiles as $profile) {
       if (!empty($_POST['profile']) && ($_POST['profile'] == $profile->name)) {
         return $profile->name;
       }
     }
 
@@ -445,19 +445,19 @@ function install_select_profile() {
  *   Array of metadata about state of form processing.
  * @param $profile_files
  *   Array of .profile files, as returned from file_scan_directory().
  */
 function install_select_profile_form(&$form_state, $profile_files) {
   $profiles = array();
   $names = array();
 
   foreach ($profile_files as $profile) {
-    include_once DRUPAL_ROOT . '/' . $profile->filename;
+    include_once DRUPAL_ROOT . '/' . $profile->filepath;
 
     // Load profile details and store them for later retrieval.
     $function = $profile->name . '_profile_details';
     if (function_exists($function)) {
       $details = $function();
     }
     $profiles[$profile->name] = $details;
 
     // Determine the name of the profile; default to file name if defined name
Index: includes/file.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/file.inc,v
retrieving revision 1.159
diff -u -9 -p -r1.159 file.inc
--- includes/file.inc	18 Feb 2009 15:19:54 -0000	1.159
+++ includes/file.inc	22 Feb 2009 13:02:26 -0000
@@ -1389,64 +1389,63 @@ function file_download() {
  *     '/(\.\.?|CVS)$/'.
  *   - 'callback'
  *     The callback function to call for each match. There is no default
  *     callback.
  *   - 'recurse'
  *     When TRUE, the directory scan will recurse the entire tree starting at
  *     the provided directory. Defaults to TRUE.
  *   - 'key'
  *     The key to be used for the returned array of files. Possible values are
- *     "filename", for the path starting with $dir, "basename", for the
- *     basename of the file, and "name" for the name of the file without an
- *     extension. Defaults to 'filename'.
+ *     'filepath', for the path starting with $dir, 'filename', for the
+ *     basename of the file, and 'name' for the name of the file without an
+ *     extension. Defaults to 'filepath'.
  *   - 'min_depth'
  *     Minimum depth of directories to return files from. Defaults to 0.
  * @param $depth
  *   Current depth of recursion. This parameter is only used internally and
  *   should not be passed.
  * @return
  *   An associative array (keyed on the provided key) of objects with
- *   "filename", "basename", and "name" members corresponding to the
- *   matching files.
+ *   'filepath', 'filename', and 'name' members corresponding to the
+ *   matching files. 
  */
 function file_scan_directory($dir, $mask, $options = array(), $depth = 0) {
   // Merge in defaults.
   $options += array(
     'nomask' => '/(\.\.?|CVS)$/',
     'callback' => 0,
     'recurse' => TRUE,
-    'key' => 'filename',
+    'key' => 'filepath',
     'min_depth' => 0,
   );
 
-  $options['key'] = (in_array($options['key'], array('filename', 'basename', 'name')) ? $options['key'] : 'filename');
+  $options['key'] = in_array($options['key'], array('filepath', 'filename', 'name')) ? $options['key'] : 'filepath';
   $files = array();
-
   if (is_dir($dir) && $handle = opendir($dir)) {
-    while (FALSE !== ($file = readdir($handle))) {
-      if (!preg_match($options['nomask'], $file) && $file[0] != '.') {
-        if (is_dir("$dir/$file") && $options['recurse']) {
+    while (FALSE !== ($filename = readdir($handle))) {
+      if (!preg_match($options['nomask'], $filename) && $filename[0] != '.') {
+        $filepath = "$dir/$filename";
+        if (is_dir($filepath) && $options['recurse']) {
           // Give priority to files in this folder by merging them in after any subdirectory files.
-          $files = array_merge(file_scan_directory("$dir/$file", $mask, $options, $depth + 1), $files);
+          $files = array_merge(file_scan_directory($filepath, $mask, $options, $depth + 1), $files);
         }
-        elseif ($depth >= $options['min_depth'] && preg_match($mask, $file)) {
+        elseif ($depth >= $options['min_depth'] && preg_match($mask, $filename)) {
           // Always use this match over anything already set in $files with the
           // same $$options['key'].
-          $filename = "$dir/$file";
-          $basename = basename($file);
-          $name = substr($basename, 0, strrpos($basename, '.'));
-          $files[${$options['key']}] = (object) array(
+          $file = (object) array(
+            'filepath' => $filepath,
             'filename' => $filename,
-            'basename' => $basename,
-            'name' => $name,
+            'name' => pathinfo($filename, PATHINFO_FILENAME),
           );
+          $key = $options['key'];
+          $files[$file->$key] = $file;
           if ($options['callback']) {
-            $options['callback']($filename);
+            $options['callback']($filepath);
           }
         }
       }
     }
 
     closedir($handle);
   }
 
   return $files;
Index: includes/install.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/install.inc,v
retrieving revision 1.84
diff -u -9 -p -r1.84 install.inc
--- includes/install.inc	18 Feb 2009 15:07:27 -0000	1.84
+++ includes/install.inc	22 Feb 2009 13:02:26 -0000
@@ -210,21 +210,21 @@ function drupal_detect_database_types() 
   $databases = array();
 
   // We define a driver as a directory in /includes/database that in turn
   // contains a database.inc file. That allows us to drop in additional drivers
   // without modifying the installer.
   // Because we have no registry yet, we need to also include the install.inc
   // file for the driver explicitly.
 
   foreach (file_scan_directory(DRUPAL_ROOT . '/includes/database', '/^[a-z]*$/i', array('recurse' => FALSE)) as $file) {
-    include_once "{$file->filename}/install.inc";
-    include_once "{$file->filename}/database.inc";
-    $drivers[$file->basename] = $file->filename;
+    include_once "{$file->filepath}/install.inc";
+    include_once "{$file->filepath}/database.inc";
+    $drivers[$file->filename] = $file->filepath;
   }
 
   foreach ($drivers as $driver => $file) {
     $class = 'DatabaseInstaller_' . $driver;
     $installer = new $class();
     if ($installer->installable()) {
       $databases[$driver] = $installer->name();
     }
   }
@@ -928,19 +928,19 @@ function drupal_check_profile($profile) 
   $function = $profile . '_profile_modules';
   $module_list = array_unique(array_merge(drupal_required_modules(), $function()));
 
   // Get a list of all .install files.
   $installs = drupal_get_install_files($module_list);
 
   // Collect requirement testing results
   $requirements = array();
   foreach ($installs as $install) {
-    require_once DRUPAL_ROOT . '/' . $install->filename;
+    require_once DRUPAL_ROOT . '/' . $install->filepath;
     $function = $install->name. '_requirements';
     if (function_exists($function)) {
       $requirements = array_merge($requirements, $function('install'));
     }
   }
   return $requirements;
 }
 
 /**
@@ -968,19 +968,19 @@ function drupal_requirements_severity(&$
  * @param $module
  *   Machine name of module to check.
  * @return
  *   TRUE/FALSE depending on the requirements are in place.
  */
 function drupal_check_module($module) {
   // Include install file
   $install = drupal_get_install_files(array($module));
   if (isset($install[$module])) {
-    require_once DRUPAL_ROOT . '/' . $install[$module]->filename;
+    require_once DRUPAL_ROOT . '/' . $install[$module]->filepath;
 
     // Check requirements
     $requirements = module_invoke($module, 'requirements', 'install');
     if (is_array($requirements) && drupal_requirements_severity($requirements) == REQUIREMENT_ERROR) {
       // Print any error messages
       foreach ($requirements as $requirement) {
         if (isset($requirement['severity']) && $requirement['severity'] == REQUIREMENT_ERROR) {
           $message = $requirement['description'];
           if (isset($requirement['value']) && $requirement['value']) {
Index: includes/locale.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/locale.inc,v
retrieving revision 1.204
diff -u -9 -p -r1.204 locale.inc
--- includes/locale.inc	18 Feb 2009 15:07:27 -0000	1.204
+++ includes/locale.inc	22 Feb 2009 13:02:26 -0000
@@ -2669,32 +2669,33 @@ function locale_batch_by_component($comp
  * @return
  *   A batch structure
  */
 function _locale_batch_build($files, $finished = NULL, $components = array()) {
   $t = get_t();
   if (count($files)) {
     $operations = array();
     foreach ($files as $file) {
       // We call _locale_batch_import for every batch operation.
-      $operations[] = array('_locale_batch_import', array($file->filename));    }
-      $batch = array(
-        'operations'    => $operations,
-        'title'         => $t('Importing interface translations'),
-        'init_message'  => $t('Starting import'),
-        'error_message' => $t('Error importing interface translations'),
-        'file'          => 'includes/locale.inc',
-        // This is not a batch API construct, but data passed along to the
-        // installer, so we know what did we import already.
-        '#components'   => $components,
-      );
-      if (isset($finished)) {
-        $batch['finished'] = $finished;
-      }
+      $operations[] = array('_locale_batch_import', array($file->filepath));
+    }
+    $batch = array(
+      'operations'    => $operations,
+      'title'         => $t('Importing interface translations'),
+      'init_message'  => $t('Starting import'),
+      'error_message' => $t('Error importing interface translations'),
+      'file'          => 'includes/locale.inc',
+      // This is not a batch API construct, but data passed along to the
+      // installer, so we know what did we import already.
+      '#components'   => $components,
+    );
+    if (isset($finished)) {
+      $batch['finished'] = $finished;
+    }
     return $batch;
   }
   return FALSE;
 }
 
 /**
  * Perform interface translation import as a batch step.
  *
  * @param $filepath
Index: includes/module.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/module.inc,v
retrieving revision 1.138
diff -u -9 -p -r1.138 module.inc
--- includes/module.inc	14 Jan 2009 12:18:37 -0000	1.138
+++ includes/module.inc	22 Feb 2009 13:02:26 -0000
@@ -95,53 +95,53 @@ function module_rebuild_cache() {
     'dependencies' => array(),
     'dependents' => array(),
     'description' => '',
     'package' => 'Other',
     'version' => NULL,
     'php' => DRUPAL_MINIMUM_PHP,
     'files' => array(),
   );
 
-  foreach ($files as $filename => $file) {
+  foreach ($files as $filepath => $file) {
     // Look for the info file.
-    $file->info = drupal_parse_info_file(dirname($file->filename) . '/' . $file->name . '.info');
+    $file->info = drupal_parse_info_file(dirname($file->filepath) . '/' . $file->name . '.info');
 
     // Skip modules that don't provide info.
     if (empty($file->info)) {
-      unset($files[$filename]);
+      unset($files[$filepath]);
       continue;
     }
     // Merge in defaults and save.
-    $files[$filename]->info = $file->info + $defaults;
+    $files[$filepath]->info = $file->info + $defaults;
 
     // Invoke hook_system_info_alter() to give installed modules a chance to
     // modify the data in the .info files if necessary.
-    drupal_alter('system_info', $files[$filename]->info, $files[$filename]);
+    drupal_alter('system_info', $files[$filepath]->info, $files[$filepath]);
 
     // Update the contents of the system table:
-    if (isset($file->status) || (isset($file->old_filename) && $file->old_filename != $file->filename)) {
+    if (isset($file->status) || (isset($file->old_filepath) && $file->old_filepath != $file->filepath)) {
       db_update('system')
         ->fields(array(
-            'info' => serialize($files[$filename]->info),
+            'info' => serialize($files[$filepath]->info),
             'name' => $file->name,
-            'filename' => $file->filename))
-        ->condition('filename', $file->old_filename)
+            'filename' => $file->filepath))
+        ->condition('filename', $file->old_filepath)
         ->execute();
     }
     else {
       // This is a new module.
-      $files[$filename]->status = 0;
+      $files[$filepath]->status = 0;
       db_insert('system')
         ->fields(array(
             'name' => $file->name,
-            'info' => serialize($files[$filename]->info),
+            'info' => serialize($files[$filepath]->info),
             'type' => 'module',
-            'filename' => $file->filename,
+            'filename' => $file->filepath,
             'status' => 0))
         ->execute();
     }
   }
   $files = _module_build_dependencies($files);
   return $files;
 }
 
 /**
@@ -529,16 +529,16 @@ function module_invoke_all() {
  */
 
 /**
  * Array of modules required by core.
  */
 function drupal_required_modules() {
   $files = drupal_system_listing('/\.info$/', 'modules', 'name', 0);
   $required = array();
   foreach ($files as $name => $file) {
-    $info = drupal_parse_info_file($file->filename);
+    $info = drupal_parse_info_file($file->filepath);
     if (!empty($info) && !empty($info['required']) && $info['required']) {
       $required[] = $name;
     }
   }
   return $required;
 }
Index: includes/registry.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/registry.inc,v
retrieving revision 1.11
diff -u -9 -p -r1.11 registry.inc
--- includes/registry.inc	20 Dec 2008 18:24:33 -0000	1.11
+++ includes/registry.inc	22 Feb 2009 13:02:26 -0000
@@ -37,19 +37,19 @@ function _registry_rebuild() {
   require_once DRUPAL_ROOT . '/includes/database/select.inc';
   require_once DRUPAL_ROOT . '/includes/database/' . $driver . '/query.inc';
 
   // Reset the resources cache.
   _registry_get_resource_name();
   // Get the list of files we are going to parse.
   $files = array();
   foreach (module_rebuild_cache() as $module) {
     if ($module->status) {
-      $dir = dirname($module->filename);
+      $dir = dirname($module->filepath);
       foreach ($module->info['files'] as $file) {
         $files["$dir/$file"] = array('module' => $module->name, 'weight' => $module->weight);
       }
     }
   }
   foreach (file_scan_directory('includes', '/\.inc$/') as $filename => $file) {
     $files["$filename"] = array('module' => '', 'weight' => 0);
   }
 
Index: includes/theme.inc
===================================================================
RCS file: /cvs/drupal/drupal/includes/theme.inc,v
retrieving revision 1.469
diff -u -9 -p -r1.469 theme.inc
--- includes/theme.inc	5 Feb 2009 03:42:56 -0000	1.469
+++ includes/theme.inc	22 Feb 2009 13:02:26 -0000
@@ -825,34 +825,34 @@ function drupal_find_theme_templates($ca
   $subtheme_paths = isset($theme_paths[$theme]) ? $theme_paths[$theme] : array();
 
   // Escape the periods in the extension.
   $regex = '/'. str_replace('.', '\.', $extension) . '$/';
   // Because drupal_system_listing works the way it does, we check for real
   // templates separately from checking for patterns.
   $files = drupal_system_listing($regex, $path, 'name', 0);
   foreach ($files as $template => $file) {
     // Ignore sub-theme templates for the current theme.
-    if (strpos($file->filename, str_replace($subtheme_paths, '', $file->filename)) !== 0) {
+    if (strpos($file->filepath, str_replace($subtheme_paths, '', $file->filepath)) !== 0) {
       continue;
     }
     // Chop off the remaining extensions if there are any. $template already
     // has the rightmost extension removed, but there might still be more,
     // such as with .tpl.php, which still has .tpl in $template at this point.
     if (($pos = strpos($template, '.')) !== FALSE) {
       $template = substr($template, 0, $pos);
     }
     // Transform - in filenames to _ to match function naming scheme
     // for the purposes of searching.
     $hook = strtr($template, '-', '_');
     if (isset($cache[$hook])) {
       $templates[$hook] = array(
         'template' => $template,
-        'path' => dirname($file->filename),
+        'path' => dirname($file->filepath),
       );
     }
     // Ensure that the pattern is maintained from base themes to its sub-themes.
     // Each sub-theme will have their templates scanned so the pattern must be
     // held for subsequent runs.
     if (isset($cache[$hook]['pattern'])) {
       $templates[$hook]['pattern'] = $cache[$hook]['pattern'];
     }
   }
@@ -866,19 +866,19 @@ function drupal_find_theme_templates($ca
       $pattern = strtr($info['pattern'], '_', '-');
 
       $matches = preg_grep('/^' . $pattern . '/', $patterns);
       if ($matches) {
         foreach ($matches as $match) {
           $file = substr($match, 0, strpos($match, '.'));
           // Put the underscores back in for the hook name and register this pattern.
           $templates[strtr($file, '-', '_')] = array(
             'template' => $file,
-            'path' => dirname($files[$match]->filename),
+            'path' => dirname($files[$match]->filepath),
             'arguments' => $info['arguments'],
           );
         }
       }
     }
   }
   return $templates;
 }
 
Index: modules/blogapi/blogapi.test
===================================================================
RCS file: /cvs/drupal/drupal/modules/blogapi/blogapi.test,v
retrieving revision 1.8
diff -u -9 -p -r1.8 blogapi.test
--- modules/blogapi/blogapi.test	30 Dec 2008 16:43:15 -0000	1.8
+++ modules/blogapi/blogapi.test	22 Feb 2009 13:02:26 -0000
@@ -62,19 +62,19 @@ class BlogAPITestCase extends DrupalWebT
       $this->assertTrue(false, 'Post found.');
 
     // Edit post.
     $content_new = $this->randomName(10);
     $result = xmlrpc($local, 'blogger.editPost', $appid, $nid, $web_user->name, $web_user->pass_raw, $content_new, TRUE);
     $this->assertTrue($result, t('Post successfully modified.'));
 
     // Upload file.
     $file = current($this->drupalGetTestFiles('text'));
-    $file_contents = file_get_contents($file->filename);
+    $file_contents = file_get_contents($file->filepath);
     $file = array();
     $file['name'] = $this->randomName() . '.txt';
     $file['type'] = 'text';
     $file['bits'] = xmlrpc_base64($file_contents);
     $result = xmlrpc($local, 'metaWeblog.newMediaObject', $blog_id, $web_user->name, $web_user->pass_raw, $file);
     $this->assertTrue($result, t('File successfully uploaded.'));
 
     $url = (array_key_exists('url', $result) ? $result['url'] : '');
 
Index: modules/simpletest/drupal_web_test_case.php
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/drupal_web_test_case.php,v
retrieving revision 1.84
diff -u -9 -p -r1.84 drupal_web_test_case.php
--- modules/simpletest/drupal_web_test_case.php	13 Feb 2009 00:39:01 -0000	1.84
+++ modules/simpletest/drupal_web_test_case.php	22 Feb 2009 13:02:26 -0000
@@ -587,35 +587,35 @@ class DrupalWebTestCase {
     // Make sure type is valid.
     if (in_array($type, array('binary', 'html', 'image', 'javascript', 'php', 'sql', 'text'))) {
      // Use original file directory instead of one created during setUp().
       $path = $this->originalFileDirectory . '/simpletest';
       $files = file_scan_directory($path, '/' . $type . '\-.*/');
 
       // If size is set then remove any files that are not of that size.
       if ($size !== NULL) {
         foreach ($files as $file) {
-          $stats = stat($file->filename);
+          $stats = stat($file->filepath);
           if ($stats['size'] != $size) {
-            unset($files[$file->filename]);
+            unset($files[$file->filepath]);
           }
         }
       }
     }
     usort($files, array($this, 'drupalCompareFiles'));
     return $files;
   }
 
   /**
    * Compare two files based on size and file name.
    */
   protected function drupalCompareFiles($file1, $file2) {
     // Determine which file is larger.
-    $compare_size = (filesize($file1->filename) > filesize($file2->filename));
+    $compare_size = (filesize($file1->filepath) > filesize($file2->filepath));
     if (!$compare_size) {
       // Both files were the same size, so return whichever one is alphabetically greater.
       return strnatcmp($file1->name, $file2->name);
     }
     else {
       // Return TRUE if $file1 is larger than $file2.
       return $compare_size;
     }
   }
Index: modules/simpletest/simpletest.install
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/simpletest.install,v
retrieving revision 1.15
diff -u -9 -p -r1.15 simpletest.install
--- modules/simpletest/simpletest.install	1 Feb 2009 17:11:00 -0000	1.15
+++ modules/simpletest/simpletest.install	22 Feb 2009 13:02:26 -0000
@@ -27,19 +27,19 @@ function simpletest_install() {
       $generated = TRUE;
     }
 
     // Copy other test files for consistency.
     $files = file_scan_directory($path, '/(html|image|javascript|php|sql)-.*/');
     if (count($files) == 0) {
       $original = drupal_get_path('module', 'simpletest') . '/files';
       $files = file_scan_directory($original, '/(html|image|javascript|php|sql)-.*/');
       foreach ($files as $file) {
-        file_unmanaged_copy($file->filename, $path . '/' . $file->basename);
+        file_unmanaged_copy($file->filepath, $path);
       }
       $generated = TRUE;
     }
 
     if ($generated) {
       drupal_set_message('Extra test files generated.');
     }
   }
 }
Index: modules/simpletest/simpletest.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/simpletest.module,v
retrieving revision 1.37
diff -u -9 -p -r1.37 simpletest.module
--- modules/simpletest/simpletest.module	20 Feb 2009 03:37:58 -0000	1.37
+++ modules/simpletest/simpletest.module	22 Feb 2009 13:02:26 -0000
@@ -459,19 +459,19 @@ function simpletest_get_all_tests() {
       $module_path = drupal_get_path('module', $module);
       $test = $module_path . "/$module.test";
       if (file_exists($test)) {
         $files[] = $test;
       }
 
       $tests_directory = $module_path . '/tests';
       if (is_dir($tests_directory)) {
         foreach (file_scan_directory($tests_directory, '/\.test$/') as $file) {
-          $files[] = $file->filename;
+          $files[] = $file->filepath;
         }
       }
     }
 
     $existing_classes = get_declared_classes();
     foreach ($files as $file) {
       include_once DRUPAL_ROOT . '/' . $file;
     }
     $classes = array_values(array_diff(get_declared_classes(), $existing_classes));
Index: modules/simpletest/tests/file.test
===================================================================
RCS file: /cvs/drupal/drupal/modules/simpletest/tests/file.test,v
retrieving revision 1.24
diff -u -9 -p -r1.24 file.test
--- modules/simpletest/tests/file.test	18 Feb 2009 15:07:27 -0000	1.24
+++ modules/simpletest/tests/file.test	22 Feb 2009 13:02:26 -0000
@@ -15,35 +15,35 @@ function file_test_validator($file, $err
 }
 
 /**
  * Helper function for testing file_scan_directory().
  *
  * Each time the function is called the file is stored in a static variable.
  * When the function is called with $reset parameter TRUE the cache is cleared
  * and the results returned.
  *
- * @param $file
- *   File object
+ * @param $filepath
+ *   File path
  * @param $reset
  *   Boolean indicating that the stored files should be removed and returned.
  * @return
  *   An array of all previous $file parameters since $reset was last called.
  */
-function file_test_file_scan_callback($file, $reset = FALSE) {
+function file_test_file_scan_callback($filepath, $reset = FALSE) {
   static $files = array();
 
   if ($reset) {
     $ret = $files;
     $files = array();
     return $ret;
   }
 
-  $files[] = $file;
+  $files[] = $filepath;
 }
 
 /**
  * Base class for file tests that adds some additional file specific
  * assertions and helper functions.
  */
 class FileTestCase extends DrupalWebTestCase {
   /**
    * Check that two files have the same values for all fields other than the
@@ -519,26 +519,26 @@ class FileSaveUploadTest extends FileHoo
     );
   }
 
   function setUp() {
     parent::setUp();
     $account = $this->drupalCreateUser(array('access content'));
     $this->drupalLogin($account);
 
     $this->image = current($this->drupalGetTestFiles('image'));
-    $this->assertTrue(is_file($this->image->filename), t("The file we're going to upload exists."));
+    $this->assertTrue(is_file($this->image->filepath), t("The file we're going to upload exists."));
 
     $this->maxFidBefore = db_query('SELECT MAX(fid) AS fid FROM {files}')->fetchField();
 
     // Upload with replace to gurantee there's something there.
     $edit = array(
       'file_test_replace' => FILE_EXISTS_REPLACE,
-      'files[file_test_upload]' => realpath($this->image->filename)
+      'files[file_test_upload]' => realpath($this->image->filepath)
     );
     $this->drupalPost('file-test/upload', $edit, t('Submit'));
     $this->assertResponse(200, t('Received a 200 response for posted test file.'));
     $this->assertRaw(t('You WIN!'), t('Found the success message.'));
 
     // Check that the correct hooks were called then clean out the hook
     // counters.
     $this->assertFileHooksCalled(array('validate', 'insert'));
     file_test_reset();
@@ -553,19 +553,19 @@ class FileSaveUploadTest extends FileHoo
     $file1 = file_load($max_fid_after);
     $this->assertTrue($file1, t('Loaded the file.'));
 
     // Reset the hook counters to get rid of the 'load' we just called.
     file_test_reset();
 
     // Upload a second file.
     $max_fid_before = db_query('SELECT MAX(fid) AS fid FROM {files}')->fetchField();
     $image2 = current($this->drupalGetTestFiles('image'));
-    $edit = array('files[file_test_upload]' => realpath($image2->filename));
+    $edit = array('files[file_test_upload]' => realpath($image2->filepath));
     $this->drupalPost('file-test/upload', $edit, t('Submit'));
     $this->assertResponse(200, t('Received a 200 response for posted test file.'));
     $this->assertRaw(t('You WIN!'));
     $max_fid_after = db_query('SELECT MAX(fid) AS fid FROM {files}')->fetchField();
 
     // Check that the correct hooks were called.
     $this->assertFileHooksCalled(array('validate', 'insert'));
 
     $file2 = file_load($max_fid_after);
@@ -578,51 +578,51 @@ class FileSaveUploadTest extends FileHoo
   }
 
 
   /**
    * Test renaming when uploading over a file that already exists.
    */
   function testExistingRename() {
     $edit = array(
       'file_test_replace' => FILE_EXISTS_RENAME,
-      'files[file_test_upload]' => realpath($this->image->filename)
+      'files[file_test_upload]' => realpath($this->image->filepath)
     );
     $this->drupalPost('file-test/upload', $edit, t('Submit'));
     $this->assertResponse(200, t('Received a 200 response for posted test file.'));
     $this->assertRaw(t('You WIN!'), t('Found the success message.'));
 
     // Check that the correct hooks were called.
     $this->assertFileHooksCalled(array('validate', 'insert'));
   }
 
   /**
    * Test replacement when uploading over a file that already exists.
    */
   function testExistingReplace() {
     $edit = array(
       'file_test_replace' => FILE_EXISTS_REPLACE,
-      'files[file_test_upload]' => realpath($this->image->filename)
+      'files[file_test_upload]' => realpath($this->image->filepath)
     );
     $this->drupalPost('file-test/upload', $edit, t('Submit'));
     $this->assertResponse(200, t('Received a 200 response for posted test file.'));
     $this->assertRaw(t('You WIN!'), t('Found the success message.'));
 
     // Check that the correct hooks were called.
     $this->assertFileHooksCalled(array('validate', 'load', 'update'));
   }
 
   /**
    * Test for failure when uploading over a file that already exists.
    */
   function testExistingError() {
     $edit = array(
       'file_test_replace' => FILE_EXISTS_ERROR,
-      'files[file_test_upload]' => realpath($this->image->filename)
+      'files[file_test_upload]' => realpath($this->image->filepath)
     );
     $this->drupalPost('file-test/upload', $edit, t('Submit'));
     $this->assertResponse(200, t('Received a 200 response for posted test file.'));
     $this->assertRaw(t('Epic upload FAIL!'), t('Found the failure message.'));
 
     // Check that the no hooks were called while failing.
     $this->assertFileHooksCalled(array());
   }
 
@@ -823,28 +823,28 @@ class FileScanDirectoryTest extends File
   function testReturn() {
     // Grab a listing of all the JavaSscript files and check that they're
     // passed to the callback.
     $all_files = file_scan_directory($this->path, '/^javascript-/');
     ksort($all_files);
     $this->assertEqual(2, count($all_files), t('Found two, expected javascript files.'));
 
     // Check the first file.
     $file = reset($all_files);
-    $this->assertEqual(key($all_files), $file->filename, t('Correct array key was used for the first returned file.'));
-    $this->assertEqual($file->filename, $this->path . '/javascript-1.txt', t('First file name was set correctly.'));
-    $this->assertEqual($file->basename, 'javascript-1.txt', t('First basename was set correctly'));
+    $this->assertEqual(key($all_files), $file->filepath, t('Correct array key was used for the first returned file.'));
+    $this->assertEqual($file->filepath, $this->path . '/javascript-1.txt', t('First file name was set correctly.'));
+    $this->assertEqual($file->filename, 'javascript-1.txt', t('First basename was set correctly'));
     $this->assertEqual($file->name, 'javascript-1', t('First name was set correctly.'));
 
     // Check the second file.
     $file = next($all_files);
-    $this->assertEqual(key($all_files), $file->filename, t('Correct array key was used for the second returned file.'));
-    $this->assertEqual($file->filename, $this->path . '/javascript-2.script', t('Second file name was set correctly.'));
-    $this->assertEqual($file->basename, 'javascript-2.script', t('Second basename was set correctly'));
+    $this->assertEqual(key($all_files), $file->filepath, t('Correct array key was used for the second returned file.'));
+    $this->assertEqual($file->filepath, $this->path . '/javascript-2.script', t('Second file name was set correctly.'));
+    $this->assertEqual($file->filename, 'javascript-2.script', t('Second basename was set correctly'));
     $this->assertEqual($file->name, 'javascript-2', t('Second name was set correctly.'));
   }
 
   /**
    * Check that the callback function is called correctly.
    */
   function testOptionCallback() {
     // When nothing is matched nothing should be passed to the callback.
     $all_files = file_scan_directory($this->path, '/^NONEXISTINGFILENAME/', array('callback' => 'file_test_file_scan_callback'));
@@ -873,25 +873,25 @@ class FileScanDirectoryTest extends File
     $this->assertEqual(1, count($filtered_files), t('Filtered correctly.'));
   }
 
   /**
    * Check that key parameter sets the return value's key.
    */
   function testOptionKey() {
     // "filename", for the path starting with $dir.
     $expected = array($this->path . '/javascript-1.txt', $this->path . '/javascript-2.script');
-    $actual = array_keys(file_scan_directory($this->path, '/^javascript-/', array('key' => 'filename')));
+    $actual = array_keys(file_scan_directory($this->path, '/^javascript-/', array('key' => 'filepath')));
     sort($actual);
     $this->assertEqual($expected, $actual, t('Returned the correct values for the filename key.'));
 
     // "basename", for the basename of the file.
     $expected = array('javascript-1.txt', 'javascript-2.script');
-    $actual = array_keys(file_scan_directory($this->path, '/^javascript-/', array('key' => 'basename')));
+    $actual = array_keys(file_scan_directory($this->path, '/^javascript-/', array('key' => 'filename')));
     sort($actual);
     $this->assertEqual($expected, $actual, t('Returned the correct values for the basename key.'));
 
     // "name" for the name of the file without an extension.
     $expected = array('javascript-1', 'javascript-2');
     $actual = array_keys(file_scan_directory($this->path, '/^javascript-/', array('key' => 'name')));
     sort($actual);
     $this->assertEqual($expected, $actual, t('Returned the correct values for the name key.'));
 
Index: modules/system/system.module
===================================================================
RCS file: /cvs/drupal/drupal/modules/system/system.module,v
retrieving revision 1.667
diff -u -9 -p -r1.667 system.module
--- modules/system/system.module	11 Feb 2009 05:33:18 -0000	1.667
+++ modules/system/system.module	22 Feb 2009 13:02:26 -0000
@@ -1056,19 +1056,20 @@ function system_check_directory($form_el
  *   An array of files to check.
  * @param $type
  *   The type of the files.
  */
 function system_get_files_database(&$files, $type) {
   // Extract current files from database.
   $result = db_query("SELECT filename, name, type, status, schema_version, weight FROM {system} WHERE type = '%s'", $type);
   while ($file = db_fetch_object($result)) {
     if (isset($files[$file->name]) && is_object($files[$file->name])) {
-      $file->old_filename = $file->filename;
+      $file->filepath = $file->filename;
+      $file->old_filepath = $file->filepath;
       foreach ($file as $key => $value) {
         if (!isset($files[$file->name]) || !isset($files[$file->name]->$key)) {
           $files[$file->name]->$key = $value;
         }
       }
     }
   }
 }
 
@@ -1149,61 +1150,62 @@ function _system_theme_data() {
     $themes = drupal_system_listing('/\.info$/', 'themes');
     // Find theme engines
     $engines = drupal_system_listing('/\.engine$/', 'themes/engines');
 
     $defaults = system_theme_default();
 
     $sub_themes = array();
     // Read info files for each theme
     foreach ($themes as $key => $theme) {
-      $themes[$key]->info = drupal_parse_info_file($theme->filename) + $defaults;
+      $themes[$key]->filename = $theme->filepath;
+      $themes[$key]->info = drupal_parse_info_file($theme->filepath) + $defaults;
 
       // Invoke hook_system_info_alter() to give installed modules a chance to
       // modify the data in the .info files if necessary.
       drupal_alter('system_info', $themes[$key]->info, $themes[$key]);
 
       if (!empty($themes[$key]->info['base theme'])) {
         $sub_themes[] = $key;
       }
       if (empty($themes[$key]->info['engine'])) {
-        $filename = dirname($themes[$key]->filename) . '/' . $themes[$key]->name . '.theme';
+        $filename = dirname($themes[$key]->filepath) . '/' . $themes[$key]->name . '.theme';
         if (file_exists($filename)) {
           $themes[$key]->owner = $filename;
           $themes[$key]->prefix = $key;
         }
       }
       else {
         $engine = $themes[$key]->info['engine'];
         if (isset($engines[$engine])) {
-          $themes[$key]->owner = $engines[$engine]->filename;
+          $themes[$key]->owner = $engines[$engine]->filepath;
           $themes[$key]->prefix = $engines[$engine]->name;
           $themes[$key]->template = TRUE;
         }
       }
 
       // Give the stylesheets proper path information.
       $pathed_stylesheets = array();
       foreach ($themes[$key]->info['stylesheets'] as $media => $stylesheets) {
         foreach ($stylesheets as $stylesheet) {
-          $pathed_stylesheets[$media][$stylesheet] = dirname($themes[$key]->filename) . '/' . $stylesheet;
+          $pathed_stylesheets[$media][$stylesheet] = dirname($themes[$key]->filepath) . '/' . $stylesheet;
         }
       }
       $themes[$key]->info['stylesheets'] = $pathed_stylesheets;
 
       // Give the scripts proper path information.
       $scripts = array();
       foreach ($themes[$key]->info['scripts'] as $script) {
-        $scripts[$script] = dirname($themes[$key]->filename) . '/' . $script;
+        $scripts[$script] = dirname($themes[$key]->filepath) . '/' . $script;
       }
       $themes[$key]->info['scripts'] = $scripts;
       // Give the screenshot proper path information.
       if (!empty($themes[$key]->info['screenshot'])) {
-        $themes[$key]->info['screenshot'] = dirname($themes[$key]->filename) . '/' . $themes[$key]->info['screenshot'];
+        $themes[$key]->info['screenshot'] = dirname($themes[$key]->filepath) . '/' . $themes[$key]->info['screenshot'];
       }
     }
 
     // Now that we've established all our master themes, go back and fill in
     // data for subthemes.
     foreach ($sub_themes as $key) {
       $base_key = system_find_base_theme($themes, $key);
       if (!$base_key) {
         continue;
Index: modules/update/update.compare.inc
===================================================================
RCS file: /cvs/drupal/drupal/modules/update/update.compare.inc,v
retrieving revision 1.15
diff -u -9 -p -r1.15 update.compare.inc
--- modules/update/update.compare.inc	20 Dec 2008 18:24:40 -0000	1.15
+++ modules/update/update.compare.inc	22 Feb 2009 13:02:26 -0000
@@ -63,19 +63,19 @@ function _update_process_info_list(&$pro
 
     // If we don't already know it, grab the change time on the .info file
     // itself. Note: we need to use the ctime, not the mtime (modification
     // time) since many (all?) tar implementations will go out of their way to
     // set the mtime on the files it creates to the timestamps recorded in the
     // tarball. We want to see the last time the file was changed on disk,
     // which is left alone by tar and correctly set to the time the .info file
     // was unpacked.
     if (!isset($file->info['_info_file_ctime'])) {
-      $info_filename = dirname($file->filename) . '/' . $file->name . '.info';
+      $info_filename = dirname($file->filepath) . '/' . $file->name . '.info';
       $file->info['_info_file_ctime'] = filectime($info_filename);
     }
 
     $project_name = $file->info['project'];
     if (!isset($projects[$project_name])) {
       // Only process this if we haven't done this project, since a single
       // project can have multiple modules or themes.
       $projects[$project_name] = array(
         'name' => $project_name,
Index: modules/upload/upload.test
===================================================================
RCS file: /cvs/drupal/drupal/modules/upload/upload.test,v
retrieving revision 1.12
diff -u -9 -p -r1.12 upload.test
--- modules/upload/upload.test	27 Jan 2009 00:22:27 -0000	1.12
+++ modules/upload/upload.test	22 Feb 2009 13:02:26 -0000
@@ -33,19 +33,19 @@ class UploadTestCase extends DrupalWebTe
     $this->drupalPost('admin/settings/uploads', $edit, t('Save configuration'));
     $this->assertText('The configuration options have been saved.', 'Upload setting saved.');
 
     $this->drupalLogout();
     $this->drupalLogin($web_user);
 
     // Create a node and attempt to attach files.
     $node = $this->drupalCreateNode();
     $text_files = $this->drupalGetTestFiles('text');
-    $files = array(current($text_files)->filename, next($text_files)->filename);
+    $files = array(current($text_files)->filepath, next($text_files)->filepath);
 
     $this->uploadFile($node, $files[0]);
     $this->uploadFile($node, $files[1]);
 
     // Check to see that uploaded file is listed in detail page and actually accessible.
     $this->assertText(basename($files[0]), basename($files[0]) . ' found on node.');
     $this->assertText(basename($files[1]), basename($files[1]) . ' found on node.');
 
     $this->checkUploadedFile(basename($files[0]));
@@ -102,39 +102,39 @@ class UploadTestCase extends DrupalWebTe
 
     $this->drupalLogin($web_user);
 
     $node = $this->drupalCreateNode();
 
     // Attempt to upload .txt file when .html is only extension allowed.
     $text_file = current($this->drupalGetTestFiles('text'));
     // Select a file that's less than the 1MB upload limit so we only test one
     // limit at a time.
-    $this->uploadFile($node, $text_file->filename, FALSE);
+    $this->uploadFile($node, $text_file->filepath, FALSE);
     // Test the error message in two steps in case there are additional errors
     // that change the error message's format.
-    $this->assertRaw(t('The specified file %name could not be uploaded.', array('%name' => $text_file->basename)), t('File %filename was not allowed to be uploaded', array('%filename' => $text_file->filename)));
+    $this->assertRaw(t('The specified file %name could not be uploaded.', array('%name' => $text_file->filename)), t('File %filepath was not allowed to be uploaded', array('%filepath' => $text_file->filepath)));
     $this->assertRaw(t('Only files with the following extensions are allowed: %files-allowed.', array('%files-allowed' => $settings['upload_extensions'])), t('File extension cited as reason for failure'));
 
     // Attempt to upload .html file when .html is only extension allowed.
     $html_files = array_values($this->drupalGetTestFiles('html'));
     // Use the HTML file with the .html extension, $html_files[0] has a .txt
     // extension.
-    $html_file = $html_files[1]->filename;
+    $html_file = $html_files[1]->filepath;
     $this->uploadFile($node, $html_file);
     $this->assertNoRaw(t('The specified file %name could not be uploaded.', array('%name' => basename($html_file))), t('File '. $html_file . ' was allowed to be uploaded'));
   }
 
   /**
    * Attempt to upload a file that is larger than the maxsize and see that it fails.
    */
   function testLimit() {
     $files = $this->drupalGetTestFiles('text', 1310720); // 1 MB.
-    $file = current($files)->filename;
+    $file = current($files)->filepath;
 
     $admin_user = $this->drupalCreateUser(array('administer site configuration'));
     $web_user = $this->drupalCreateUser(array('access content', 'edit any page content', 'upload files', 'view uploaded files'));
 
     $this->drupalLogin($admin_user);
 
     // Setup upload settings.
     $settings = array();
     $settings['upload_list'] = '1'; // Yes.
Index: modules/user/user.test
===================================================================
RCS file: /cvs/drupal/drupal/modules/user/user.test,v
retrieving revision 1.28
diff -u -9 -p -r1.28 user.test
--- modules/user/user.test	9 Feb 2009 07:36:15 -0000	1.28
+++ modules/user/user.test	22 Feb 2009 13:02:26 -0000
@@ -529,19 +529,19 @@ class UserPictureTestCase extends Drupal
    *
    * results: The image should be uploaded because ImageGDToolkit resizes the picture
    */
   function testWithGDinvalidDimension() {
     if ($this->_directory_test)
       if (image_get_toolkit()) {
         $this->drupalLogin($this->user);
 
         $image = current($this->drupalGetTestFiles('image'));
-        $info = image_get_info($image->filename);
+        $info = image_get_info($image->filepath);
 
         // Set new variables: invalid dimensions, valid filesize (0 = no limit).
         $test_dim = ($info['width'] - 10) . 'x' . ($info['height'] - 10);
         variable_set('user_picture_dimensions', $test_dim);
         variable_set('user_picture_file_size', 0);
 
         $pic_path = $this->saveUserPicture($image);
         // Check that the image was resized and is being displayed on the
         // user's profile page.
@@ -563,32 +563,32 @@ class UserPictureTestCase extends Drupal
    * results: The image should be uploaded because ImageGDToolkit resizes the picture
    */
   function testWithGDinvalidSize() {
     if ($this->_directory_test)
       if (image_get_toolkit()) {
 
         $this->drupalLogin($this->user);
 
         $image = current($this->drupalGetTestFiles('image'));
-        $info = image_get_info($image->filename);
+        $info = image_get_info($image->filepath);
 
         // Set new variables: valid dimensions, invalid filesize.
         $test_dim = ($info['width'] + 10) . 'x' . ($info['height'] + 10);
         $test_size = 1;
         variable_set('user_picture_dimensions', $test_dim);
         variable_set('user_picture_file_size', $test_size);
 
         $pic_path = $this->saveUserPicture($image);
 
         // Test that the upload failed and that the correct reason was cited.
-        $text = t('The specified file %filename could not be uploaded.', array('%filename' => $image->basename));
+        $text = t('The specified file %filename could not be uploaded.', array('%filename' => $image->filename));
         $this->assertRaw($text, t('Upload failed.'));
-        $text = t('The file is %filesize exceeding the maximum file size of %maxsize.', array('%filesize' => format_size(filesize($image->filename)), '%maxsize' => format_size($test_size * 1024)));
+        $text = t('The file is %filesize exceeding the maximum file size of %maxsize.', array('%filesize' => format_size(filesize($image->filepath)), '%maxsize' => format_size($test_size * 1024)));
         $this->assertRaw($text, t('File size cited as reason for failure.'));
 
         // Check if file is not uploaded.
         $this->assertFalse(is_file($pic_path), t('File was not uploaded.'));
       }
   }
 
   /**
    * Do the test:
@@ -598,29 +598,29 @@ class UserPictureTestCase extends Drupal
    * results: The image shouldn't be uploaded
    */
    function testWithoutGDinvalidDimension() {
     if ($this->_directory_test)
       if (!image_get_toolkit()) {
 
         $this->drupalLogin($this->user);
 
         $image = current($this->drupalGetTestFiles('image'));
-        $info = image_get_info($image->filename);
+        $info = image_get_info($image->filepath);
 
         // Set new variables: invalid dimensions, valid filesize (0 = no limit).
         $test_dim = ($info['width'] - 10) . 'x' . ($info['height'] - 10);
         variable_set('user_picture_dimensions', $test_dim);
         variable_set('user_picture_file_size', 0);
 
         $pic_path = $this->saveUserPicture($image);
 
         // Test that the upload failed and that the correct reason was cited.
-        $text = t('The specified file %filename could not be uploaded.', array('%filename' => $image->basename));
+        $text = t('The specified file %filename could not be uploaded.', array('%filename' => $image->filename));
         $this->assertRaw($text, t('Upload failed.'));
         $text = t('The image is too large; the maximum dimensions are %dimensions pixels.', array('%dimensions' => $test_dim));
         $this->assertRaw($text, t('Checking response on invalid image (dimensions).'));
 
         // Check if file is not uploaded.
         $this->assertFalse(is_file($pic_path), t('File was not uploaded.'));
       }
    }
 
@@ -631,73 +631,73 @@ class UserPictureTestCase extends Drupal
    *
    * results: The image shouldn't be uploaded
    */
    function testWithoutGDinvalidSize() {
     if ($this->_directory_test)
       if (!image_get_toolkit()) {
         $this->drupalLogin($this->user);
 
         $image = current($this->drupalGetTestFiles('image'));
-        $info = image_get_info($image->filename);
+        $info = image_get_info($image->filepath);
 
         // Set new variables: valid dimensions, invalid filesize.
         $test_dim = ($info['width'] + 10) . 'x' . ($info['height'] + 10);
         $test_size = 1;
         variable_set('user_picture_dimensions', $test_dim);
         variable_set('user_picture_file_size', $test_size);
 
         $pic_path = $this->saveUserPicture($image);
 
         // Test that the upload failed and that the correct reason was cited.
-        $text = t('The specified file %filename could not be uploaded.', array('%filename' => $image->basename));
+        $text = t('The specified file %filename could not be uploaded.', array('%filename' => $image->filename));
         $this->assertRaw($text, t('Upload failed.'));
-        $text = t('The file is %filesize exceeding the maximum file size of %maxsize.', array('%filesize' => format_size(filesize($image->filename)), '%maxsize' => format_size($test_size * 1024)));
+        $text = t('The file is %filesize exceeding the maximum file size of %maxsize.', array('%filesize' => format_size(filesize($image->filepath)), '%maxsize' => format_size($test_size * 1024)));
         $this->assertRaw($text, t('File size cited as reason for failure.'));
 
         // Check if file is not uploaded.
         $this->assertFalse(is_file($pic_path), t('File was not uploaded.'));
       }
   }
 
   /**
    * Do the test:
    *  Picture is valid (proper size and dimension)
    *
    * results: The image should be uploaded
    */
   function testPictureIsValid() {
     if ($this->_directory_test) {
       $this->drupalLogin($this->user);
 
       $image = current($this->drupalGetTestFiles('image'));
-      $info = image_get_info($image->filename);
+      $info = image_get_info($image->filepath);
 
       // Set new variables: valid dimensions, valid filesize (0 = no limit).
       $test_dim = ($info['width'] + 10) . 'x' . ($info['height'] + 10);
       variable_set('user_picture_dimensions', $test_dim);
       variable_set('user_picture_file_size', 0);
 
       $pic_path = $this->saveUserPicture($image);
 
       // Check if image is displayed in user's profile page.
       $this->drupalGet('user');
       $this->assertRaw($pic_path, t("Image is displayed in user's profile page"));
 
       // Check if file is located in proper directory.
       $this->assertTrue(is_file($pic_path), t('File is located in proper directory'));
     }
   }
 
   function saveUserPicture($image) {
-    $edit = array('files[picture_upload]' => realpath($image->filename));
+    $edit = array('files[picture_upload]' => realpath($image->filepath));
     $this->drupalPost('user/' . $this->user->uid.'/edit', $edit, t('Save'));
 
-    $img_info = image_get_info($image->filename);
+    $img_info = image_get_info($image->filepath);
     $picture_dir = variable_get('user_picture_path', 'pictures');
     $pic_path = file_directory_path() . '/' . $picture_dir . '/picture-' . $this->user->uid . '.' . $img_info['extension'];
 
     return $pic_path;
   }
 }
 
 
 class UserPermissionsTestCase extends DrupalWebTestCase {