Index: comment.inc
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/project_issue/comment.inc,v
retrieving revision 1.149
diff -u -F^f -u -F^f -r1.149 comment.inc
--- comment.inc	18 Feb 2009 19:53:32 -0000	1.149
+++ comment.inc	19 Feb 2009 07:02:17 -0000
@@ -554,19 +554,10 @@ function project_issue_update_by_comment
 function project_issue_change_comment_upload_path(&$comment) {
   static $run = NULL;
 
-  $node = node_load($comment['nid']);
-  if (isset($comment['files']) && !isset($run)) {
+  // Only for new comments with attachments.
+  if (empty($comment['cid']) && isset($comment['files']) && !isset($run)) {
     $run = TRUE;  // Make sure this only gets run once.
-    $issue_dir = variable_get('project_directory_issues', 'issues');
-    foreach ($comment['files'] as $key => $file) {
-      if ($issue_dir && 0 === strpos($key, 'upload_')) {  // Only rewrite the name when adding the file, not when updating it
-        // Change where the file will be saved to the specified directory.
-        // Since changes to the comment aren't carried to submit, we have
-        // to adjust $form_values here.
-        $filename = $issue_dir .'/'. $comment['files'][$key]['filename'];
-        form_set_value(array('#parents' => array('files', $key, 'filename')), $filename, $form_state);
-      }
-    }
+    project_issue_rewrite_issue_filepath($comment['files']);
   }
 }
 
Index: project_issue.module
===================================================================
RCS file: /cvs/drupal-contrib/contributions/modules/project_issue/project_issue.module,v
retrieving revision 1.137
diff -u -F^f -u -F^f -r1.137 project_issue.module
--- project_issue.module	19 Feb 2009 01:17:39 -0000	1.137
+++ project_issue.module	19 Feb 2009 07:02:18 -0000
@@ -912,16 +912,9 @@ function project_issue_issue_nodeapi(&$n
       project_issue_comment_view($node);
       break;
     case 'presave':
-      if (isset($node->files)) {
-        $issue_dir = variable_get('project_directory_issues', 'issues');
-        foreach ($node->files as $key => $file) {
-          // Only rewrite the name when an issues directory exists, and when
-          // adding the file, not when updating it.
-          if ($issue_dir && 0 === strpos($key, 'upload_')) {
-            // Change where the file will be saved to the specified directory.
-            $node->files[$key]['filename'] = $issue_dir .'/'. $node->files[$key]['filename'];
-          }
-        }
+      // Only for new nodes with files set.
+      if (empty($node->nid) && isset($node->files)) {
+        project_issue_rewrite_issue_filepath($node->files);
       }
       break;
     case 'insert':
@@ -976,6 +969,26 @@ function project_issue_exit() {
   }
 }
 
+/**
+ * Rewrites the file information to move files to the issues directory.
+ *
+ * @param $files
+ *   An array of file objects, keyed by file ID.
+ */
+function project_issue_rewrite_issue_filepath($files) {
+  if ($issue_dir = variable_get('project_directory_issues', 'issues') ) {
+    foreach ($files as $key => $file) {
+      $file = (object) $file;
+      $old_path = $file->filepath;
+      $final_dir = file_directory_path() .'/'. $issue_dir;
+      $move_path = $old_path;
+      file_move($move_path, $final_dir .'/'. basename($file->filepath));
+      $new_basename = basename($move_path);
+      db_query("UPDATE {files} SET filepath = '%s' WHERE fid = %d", $final_dir .'/'. $new_basename, $file->fid);
+    }
+  }
+}
+
 function project_issue_my_projects_table() {
   $uid = 0;
   $display = views_get_page_view();