diff --git a/coder_upgrade/CHANGELOG.txt b/coder_upgrade/CHANGELOG.txt
index 15fd749876d1a50c910de7a11be04b6fc87ff9cd..077e08a87921b8247085db899a681ca1d877a27d 100644
--- a/coder_upgrade/CHANGELOG.txt
+++ b/coder_upgrade/CHANGELOG.txt
@@ -2,6 +2,14 @@
 
 coder_upgrade 7.x-1.x, 2009-xx-xx (development version)
 ---------------------------------
+- Changes (2010-11-19):
+  * coder_upgrade.main.inc
+  * - #245471 (comment #7): remove base directory path from patch file in coder_upgrade_make_patch_file()
+  * inc, install, help.inc, main.inc, module, test
+  * - refactor file_directory_path() references to coder_upgrade_directory_path()
+  * coder_upgrade.run.php
+  * - add php memory and time limits
+
 - Changes (2010-10-30):
   * coder_upgrade.module
   * - refactor form submission code to coder_upgrade_conversions_apply()
diff --git a/coder_upgrade/coder_upgrade.help.inc b/coder_upgrade/coder_upgrade.help.inc
index 25c0595fa47b0897766a291c469727339d3e91f9..509f629ca15418ee0a561148b65a7d1d9a79802b 100644
--- a/coder_upgrade/coder_upgrade.help.inc
+++ b/coder_upgrade/coder_upgrade.help.inc
@@ -12,8 +12,8 @@
  * Implements hook_help().
  */
 function coder_upgrade_help($path, $arg) {
-  $input = file_directory_path() . '/' . variable_get('coder_upgrade_dir_old', DEADWOOD_OLD);
-  $output = file_directory_path() . '/' . variable_get('coder_upgrade_dir_new', DEADWOOD_NEW);
+  $input = coder_upgrade_directory_path('old', FALSE);
+  $output = coder_upgrade_directory_path('new', FALSE);
   switch ($path) {
     case 'admin/config/development/coder/upgrade/settings':
       return tp('This is a list of the variables used by the automated module conversion suite.');
diff --git a/coder_upgrade/coder_upgrade.inc b/coder_upgrade/coder_upgrade.inc
index 03b6c6a10b769b53dfd682f8de1cb54b27824a4f..af350010560f0409bcbe33b1133f1f05e5e49c76 100644
--- a/coder_upgrade/coder_upgrade.inc
+++ b/coder_upgrade/coder_upgrade.inc
@@ -92,6 +92,39 @@ function coder_upgrade_clean_directory($path, $remove_me = FALSE) {
   }
 }
 
+/**
+ * Returns full directory path relative to sites directory.
+ *
+ * @param string $name
+ *   Name of the directory.
+ * @param boolean $add_slash
+ *   Indicates whether to add a trailing slash.
+ * @param boolean $stream_format
+ *   Indicates whether to use the actual path or a stream protocol.
+ * @return string
+ *   A string of the directory path.
+ */
+function coder_upgrade_directory_path($name, $add_slash = TRUE, $stream_format = FALSE) {
+  $slash = $add_slash ? '/' : '';
+  $prefix_no_slash = $stream_format ? file_default_scheme() . ':/' : file_directory_path();
+  $prefix = $prefix_no_slash . '/';
+
+  switch ($name) {
+    case 'base':
+      return $prefix . variable_get('coder_upgrade_dir', DEADWOOD_DIR) . $slash;
+    case 'old':
+      return $prefix . variable_get('coder_upgrade_dir_old', DEADWOOD_OLD) . $slash;
+    case 'new':
+      return $prefix . variable_get('coder_upgrade_dir_new', DEADWOOD_NEW) . $slash;
+    case 'patch':
+      return $prefix . variable_get('coder_upgrade_dir_patch', DEADWOOD_PATCH) . $slash;
+    case '':
+      return $prefix_no_slash; // @todo Is this correct with a stream format?
+    default:
+      return $prefix . $name . $slash;
+  }
+}
+
 /**
  * Returns the local public directory path.
  *
@@ -127,10 +160,6 @@ if (!function_exists('file_directory_path')) {
 if (!function_exists('drupal_get_path')) {
   function drupal_get_path($type, $name) {
     global $modules_base;
-
-//     if ($name == 'coder_upgrade') {
-//       $name = 'coder/coder_upgrade';
-//     }
     return $modules_base . "/$name";
   }
 }
diff --git a/coder_upgrade/coder_upgrade.install b/coder_upgrade/coder_upgrade.install
index f72c0c1b3f2cfb5ee508086f5c27ca88cb0f7b8c..c52fd792fcd131dfb685b7ebfb715a888db235bd 100644
--- a/coder_upgrade/coder_upgrade.install
+++ b/coder_upgrade/coder_upgrade.install
@@ -17,19 +17,19 @@ function coder_upgrade_install() {
   // Create the top-level module directory.
   // Because the core function is now recursive, we could start with the
   // subdirectories. However, this code is clean and allows for one else block.
-  $dir = file_directory_path() . '/' . DEADWOOD_DIR;
+  $dir = coder_upgrade_directory_path('base', FALSE);
   if (file_prepare_directory($dir, FILE_CREATE_DIRECTORY)) {
     // Create the old and new module directories.
-    $dir = file_directory_path() . '/' . DEADWOOD_OLD;
+    $dir = coder_upgrade_directory_path('old', FALSE);
     if (!file_prepare_directory($dir, FILE_CREATE_DIRECTORY)) {
       drupal_set_message(st('The files directory at %directory can not be written to. This is the default directory searched by Coder Upgrade for modules to be converted.', array('%directory' => $dir)), 'error');
     }
-    $dir = file_directory_path() . '/' . DEADWOOD_NEW;
+    $dir = coder_upgrade_directory_path('new', FALSE);
       if (!file_prepare_directory($dir, FILE_CREATE_DIRECTORY)) {
         drupal_set_message(st('The files directory at %directory can not be written to. This is the default directory to which Coder Upgrade writes converted module code.', array('%directory' => $dir)), 'error');
     }
     // Create the patch directory.
-    $dir = file_directory_path() . '/' . DEADWOOD_PATCH;
+    $dir = coder_upgrade_directory_path('patch', FALSE);
     if (!file_prepare_directory($dir, FILE_CREATE_DIRECTORY)) {
       drupal_set_message(st('The files directory at %directory can not be written to. This is the default directory to which Coder Upgrade writes patch files.', array('%directory' => $dir)), 'error');
     }
@@ -48,11 +48,11 @@ function coder_upgrade_install() {
  */
 function coder_upgrade_uninstall() {
   // Remove the module input and output directories.
-  $dir = file_directory_path() . '/' . variable_get('coder_upgrade_dir_old', DEADWOOD_OLD);
+  $dir = coder_upgrade_directory_path('old', FALSE);
   coder_upgrade_clean_directory($dir, TRUE);
-  $dir = file_directory_path() . '/' . variable_get('coder_upgrade_dir_new', DEADWOOD_NEW);
+  $dir = coder_upgrade_directory_path('new', FALSE);
   coder_upgrade_clean_directory($dir, TRUE);
-  $dir = file_directory_path() . '/' . variable_get('coder_upgrade_dir_patch', DEADWOOD_PATCH);
+  $dir = coder_upgrade_directory_path('patch', FALSE);
   coder_upgrade_clean_directory($dir, TRUE);
 
   // Remove items from {variables} table.
@@ -87,7 +87,7 @@ function coder_upgrade_requirements($phase) {
         'severity' => REQUIREMENT_ERROR
       );
     }
-    $dir = file_directory_path();
+    $dir = coder_upgrade_directory_path('', FALSE);
     if (!file_prepare_directory($dir, FILE_CREATE_DIRECTORY)) {
       $requirements['coder_upgrade_files'] = array(
         'title' => $t('Files directory'),
@@ -97,7 +97,7 @@ function coder_upgrade_requirements($phase) {
     }
   }
   else {
-    $dir = file_directory_path() . '/' . variable_get('coder_upgrade_dir_new', DEADWOOD_NEW);
+    $dir = coder_upgrade_directory_path('new', FALSE);
     if (!file_prepare_directory($dir, FILE_CREATE_DIRECTORY)) {
       $requirements['coder_upgrade_files'] = array(
         'title' => $t('Coder Upgrade directory'),
diff --git a/coder_upgrade/coder_upgrade.module b/coder_upgrade/coder_upgrade.module
index 9ab4e87e8099b99dd4c4bed4235fb85cb2e398b7..b4a4477a60e1c4d1ccaeff6d3e309b3b0cacea55 100644
--- a/coder_upgrade/coder_upgrade.module
+++ b/coder_upgrade/coder_upgrade.module
@@ -100,7 +100,7 @@ function coder_upgrade_settings_form($form, &$form_state) {
   module_load_include('inc', 'coder_upgrade', 'conversions/coder_upgrade.main');
   $parser = new PGPParser();
 
-  $path = file_directory_path();
+  $path = coder_upgrade_directory_path('', FALSE);
   $form['coder_upgrade_dir'] = array(
     '#title' => t('Module base directory'),
     '#type' => 'textfield',
@@ -185,7 +185,7 @@ function coder_upgrade_settings_form_submit($form, &$form_state) {
   $cur = variable_get('coder_upgrade_dir', DEADWOOD_DIR);
   $new = $op == t('Reset to defaults') ? DEADWOOD_DIR : $values['coder_upgrade_dir'];
   if ($new != $cur) {
-    if (rename(file_directory_path() . '/' . $cur, file_directory_path() . '/' . $new)) {
+    if (rename(coder_upgrade_directory_path($cur, FALSE), coder_upgrade_directory_path($new, FALSE))) {
       variable_set('coder_upgrade_dir_old', $new . '/old');
       variable_set('coder_upgrade_dir_new', $new . '/new');
       variable_set('coder_upgrade_dir_patch', $new . '/patch');
@@ -369,7 +369,7 @@ function coder_upgrade_extensions_build(&$extensions) {
 function coder_upgrade_directories_build(&$directories) {
   // Build the directory list.
   $deadwood_dir = variable_get('coder_upgrade_dir_old', DEADWOOD_OLD);
-  $path = realpath(file_directory_path() . '/' . $deadwood_dir);
+  $path = realpath(coder_upgrade_directory_path('old', FALSE));
   $dirs = coder_upgrade_scan_directory($path);
   if (!$dirs) {
     drupal_set_message(t('Please place modules to be converted in @path.', array('@path' => $path)), 'error');
@@ -510,10 +510,10 @@ function coder_upgrade_conversions_apply($form_state) {
   module_load_include('inc', 'coder_upgrade', 'conversions/coder_upgrade.main');
   if (variable_get('coder_upgrade_use_separate_process', TRUE)) {
     // Conversion code will be run in a separate process.
-    drupal_set_message('Conversion code will be run in a separate process.');
+    drupal_set_message('Module conversion code will run in a separate process.');
     $path = coder_upgrade_parameters_save($upgrades, $extensions, $items);
     $script = drupal_get_path('module', 'coder_upgrade') . '/scripts/coder_upgrade.run.php';
-//     $output = file_directory_path() . '/coder_upgrade/coder-upgrade-run.txt';
+//     $output = coder_upgrade_directory_path('base') . 'coder-upgrade-run.txt';
     $command = "php $script -- file=$path 2>&1"; // $command = "php $script -- file=$path > $output 2>&1";
     // Execute the command and capture the output.
     $output = shell_exec($command);
@@ -524,7 +524,7 @@ function coder_upgrade_conversions_apply($form_state) {
   }
   else {
     // Conversion code will be run in the same process.
-    drupal_set_message('Conversion code will be run in the same process.');
+    drupal_set_message('Module conversion code will run in the same process.');
     $success = coder_upgrade_start($upgrades, $extensions, $items);
   }
 
@@ -546,8 +546,8 @@ function coder_upgrade_conversions_prepare($form_state) {
     );
   }
 
-  $old_dir = DRUPAL_ROOT . '/' . file_directory_path() . '/' . variable_get('coder_upgrade_dir_old', DEADWOOD_OLD) . '/';
-  $new_dir = DRUPAL_ROOT . '/' . file_directory_path() . '/' . variable_get('coder_upgrade_dir_new', DEADWOOD_NEW) . '/';
+  $old_dir = DRUPAL_ROOT . '/' . coder_upgrade_directory_path('old');
+  $new_dir = DRUPAL_ROOT . '/' . coder_upgrade_directory_path('new');
 
   // Combine directory and module items into a single list.
   // Omit name from key so as to allow for duplicate names.
@@ -595,8 +595,8 @@ function coder_upgrade_parameters_save($upgrades, $extensions, $items) {
   }
   // Create paths array.
   $paths = array(
-    'files_base' => file_directory_path(),
-    'modules_base' => str_replace('files', 'modules', file_directory_path()),
+    'files_base' => coder_upgrade_directory_path('', FALSE),
+    'modules_base' => str_replace('files', 'modules', coder_upgrade_directory_path('', FALSE)),
   );
   // Create variables array.
   $variables = array(
@@ -793,7 +793,7 @@ function coder_upgrade_patch_path($filename) {
   static $dirname = '';
 
   if (!$dirname) {
-    $dirname = file_directory_path() . '/' . variable_get('coder_upgrade_dir_patch', DEADWOOD_PATCH);
+    $dirname = coder_upgrade_directory_path('patch');
   }
-  return $dirname . "/$filename";
+  return $dirname . "$filename";
 }
diff --git a/coder_upgrade/coder_upgrade.test b/coder_upgrade/coder_upgrade.test
index 5698fcb2619aa6df2025c0159e5212d9b5b9de84..a1d6d93a8bda3e6bd5f64702b139ae661feb1c19 100644
--- a/coder_upgrade/coder_upgrade.test
+++ b/coder_upgrade/coder_upgrade.test
@@ -40,7 +40,7 @@ class CoderUpgradeUnitTestCase extends DrupalUnitTestCase {
     $this->captureThemeInfo();
     file_put_contents('output.html', "after captureThemeInfo\n", FILE_APPEND);
     // Save the live site files directory path.
-    $this->site_directory = DRUPAL_ROOT . '/' . file_directory_path() . '/' . variable_get('coder_upgrade_dir_new', DEADWOOD_NEW) . '/';
+    $this->site_directory = DRUPAL_ROOT . '/' . coder_upgrade_directory_path('new');
     file_put_contents('output.html', $this->site_directory . "\n", FILE_APPEND);
 
     parent::setUp('grammar_parser', 'coder_upgrade');
@@ -79,7 +79,7 @@ class CoderUpgradeUnitTestCase extends DrupalUnitTestCase {
     coder_upgrade_debug_print("module = $module_dirname");
 
     $in_dirname = $module_dirname . '/tests/old/';
-    $out_dirname = DRUPAL_ROOT . '/' . file_directory_path() . '/' . variable_get('coder_upgrade_dir_new', DEADWOOD_NEW) . '/';
+    $out_dirname = DRUPAL_ROOT . '/' . coder_upgrade_directory_path('new');
 
     $directories = array($this->test_directory => 1);
     foreach ($directories as $key => $directory) {
@@ -111,7 +111,7 @@ class CoderUpgradeUnitTestCase extends DrupalUnitTestCase {
     $module_dirname = DRUPAL_ROOT . '/' . drupal_get_path('module', 'coder_upgrade');
     $in_dirname = $module_dirname . '/tests/old/';
     $expected_dirname = $module_dirname . '/tests/new/';
-    $out_dirname = DRUPAL_ROOT . '/' . file_directory_path() . '/' . variable_get('coder_upgrade_dir_new', DEADWOOD_NEW) . '/';
+    $out_dirname = DRUPAL_ROOT . '/' . coder_upgrade_directory_path('new');
     file_put_contents('output.html', "$out_dirname\n", FILE_APPEND);
 
     $upgrades = coder_upgrade_upgrade_info();
diff --git a/coder_upgrade/conversions/coder_upgrade.main.inc b/coder_upgrade/conversions/coder_upgrade.main.inc
index f6a641b38579aa21be762240bead6368385e421d..1fbdb588b506a50092113a20c22dcbe78c7c7fdc 100644
--- a/coder_upgrade/conversions/coder_upgrade.main.inc
+++ b/coder_upgrade/conversions/coder_upgrade.main.inc
@@ -551,7 +551,7 @@ function coder_upgrade_module_name($dirname, &$item) {
  */
 function coder_upgrade_make_patch_file($item, $replace_files = FALSE) {
   // Patch directory.
-  $patch_dir = file_directory_path() . '/' . variable_get('coder_upgrade_dir_patch', DEADWOOD_PATCH) . '/';
+  $patch_dir = coder_upgrade_directory_path('patch');
 
   // Make a patch file.
   coder_upgrade_log_print("\n*************************");
@@ -563,6 +563,12 @@ function coder_upgrade_make_patch_file($item, $replace_files = FALSE) {
   $new_dir = $replace_files ? $item['old_dir'] : $item['new_dir'];
   coder_upgrade_log_print("Making patch file: diff -up -r {$old_dir} {$new_dir} > {$patch_filename}");
   shell_exec("diff -up -r {$old_dir} {$new_dir} > {$patch_filename}");
+
+  // Remove the path strings from the patch file (for usability purposes).
+  $old1 = $old_dir . '/';
+  $new1 = $new_dir . '/';
+  $contents = file_get_contents($patch_filename);
+  file_put_contents($patch_filename, str_replace(array($old1, $new1), '', $contents));
 }
 
 /**
@@ -751,7 +757,7 @@ function coder_upgrade_path($type = '') {
   static $path = '';
 
   if (!$path) {
-    $path = file_directory_path() . '/' . variable_get('coder_upgrade_dir', DEADWOOD_DIR);
+    $path = coder_upgrade_directory_path('base', FALSE);
   }
   return $type ? $path . '/' . $type . '.txt' : $path;
 }
diff --git a/coder_upgrade/scripts/coder_upgrade.run.php b/coder_upgrade/scripts/coder_upgrade.run.php
index 0de9a57f2564c626da1d0c3cb584f4b288321795..7fc87361fc2ca9ffbedd94bab339e95918fcd2c8 100644
--- a/coder_upgrade/scripts/coder_upgrade.run.php
+++ b/coder_upgrade/scripts/coder_upgrade.run.php
@@ -44,6 +44,8 @@ echo 'Curr 1: ' . number_format(memory_get_usage(TRUE), 0, '.', ',') . " bytes\n
 define('DRUPAL_ROOT', getcwd());
 
 ini_set('display_errors', 1);
+ini_set('memory_limit', '128M');
+ini_set('max_execution_time', 180);
 set_error_handler("error_handler");
 set_exception_handler("exception_handler");
 
@@ -126,13 +128,18 @@ function extract_arguments() {
       break;
 
     case 'cli':
-      if ($_SERVER['argc'] < 3) {
+      $skip_args = 2;
+      if ($_SERVER['argc'] == 2) {
+        $skip_args = 1;
+      }
+      elseif ($_SERVER['argc'] < 2) {
         echo 'file parameter is not set' . "\n";
         return;
       }
       foreach ($_SERVER['argv'] as $index => $arg) {
-        // First two arguments are script filename and '--'.
-        if ($index < 2) continue;
+        // First two arguments are usually script filename and '--'.
+        // Sometimes the '--' is omitted.
+        if ($index < $skip_args) continue;
         list($key, $value) = explode('=', $arg);
         $arguments[$key] = $value;
       }